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Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
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Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
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Honeker LK, Pugliese G, Ingrisch J, Fudyma J, Gil-Loaiza J, Carpenter E, Singer E, Hildebrand G, Shi L, Hoyt DW, Chu RK, Toyoda J, Krechmer JE, Claflin MS, Ayala-Ortiz C, Freire-Zapata V, Pfannerstill EY, Daber LE, Meeran K, Dippold MA, Kreuzwieser J, Williams J, Ladd SN, Werner C, Tfaily MM, Meredith LK. Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nat Microbiol 2023; 8:1480-1494. [PMID: 37524975 PMCID: PMC10390333 DOI: 10.1038/s41564-023-01432-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/19/2023] [Indexed: 08/02/2023]
Abstract
Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking 13C from position-specific 13C-pyruvate into CO2 and VOCs in parallel with multi-omics. During drought, efflux of 13C-enriched acetate, acetone and C4H6O2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,13C-CO2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.
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Affiliation(s)
- Linnea K Honeker
- Biosphere 2, University of Arizona, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Giovanni Pugliese
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - Johannes Ingrisch
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Jane Fudyma
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | | | | | - Gina Hildebrand
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Lingling Shi
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - David W Hoyt
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason Toyoda
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jordan E Krechmer
- Aerodyne Research, Inc., Billerica, MA, USA
- Bruker Daltonics Inc., Billerica, MA, USA
| | | | | | | | - Eva Y Pfannerstill
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - L Erik Daber
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | | | - Michaela A Dippold
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Jürgen Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Jonathan Williams
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - S Nemiah Ladd
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Christiane Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Malak M Tfaily
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Laura K Meredith
- Biosphere 2, University of Arizona, Tucson, AZ, USA.
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA.
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3
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Hestrin R, Kan M, Lafler M, Wollard J, Kimbrel JA, Ray P, Blazewicz SJ, Stuart R, Craven K, Firestone M, Nuccio EE, Pett-Ridge J. Plant-associated fungi support bacterial resilience following water limitation. THE ISME JOURNAL 2022; 16:2752-2762. [PMID: 36085516 PMCID: PMC9666503 DOI: 10.1038/s41396-022-01308-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H218O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis compared to S. bescii-inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought susceptible. Overall, H218O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.
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Affiliation(s)
- Rachel Hestrin
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA.
| | - Megan Kan
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Marissa Lafler
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jessica Wollard
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jeffrey A Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Prasun Ray
- Department of Natural Resources, University of Maryland Eastern Shore, Princess Anne, MD, USA
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
| | - Steven J Blazewicz
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Rhona Stuart
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Kelly Craven
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA.
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4
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Affiliation(s)
| | | | - Erland Bååth
- Section of Microbial Ecology Department of Biology Lund University 22362 Lund Sweden
| | - Patrick Meir
- School of Geosciences University of Edinburgh Crew Building, Kings Buildings Edinburgh UK
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5
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Sokol NW, Whalen ED, Jilling A, Kallenbach C, Pett‐Ridge J, Georgiou K. The Global Distribution, Formation, and Fate of Mineral‐Associated Soil Organic Matter Under a Changing Climate – A Trait‐Based Perspective. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah W. Sokol
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California USA
| | - Emily D. Whalen
- Department of Natural Resources and the En]vironment University of New Hampshire Durham New Hampshire USA
| | - Andrea Jilling
- College of Agriculture Oklahoma State University Stillwater Oklahoma USA
| | - Cynthia Kallenbach
- Department of Natural Resources Sciences McGill University Montreal Quebec Canada
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California USA
- Life & Environmental Sciences Department University of California Merced Merced California USA
| | - Katerina Georgiou
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California USA
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6
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Benaffari W, Boutasknit A, Anli M, Ait-El-Mokhtar M, Ait-Rahou Y, Ben-Laouane R, Ben Ahmed H, Mitsui T, Baslam M, Meddich A. The Native Arbuscular Mycorrhizal Fungi and Vermicompost-Based Organic Amendments Enhance Soil Fertility, Growth Performance, and the Drought Stress Tolerance of Quinoa. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030393. [PMID: 35161374 PMCID: PMC8838481 DOI: 10.3390/plants11030393] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 05/17/2023]
Abstract
The present study aimed to determine the effects of biostimulants on the physicochemical parameters of the agricultural soil of quinoa under two water regimes and to understand the mode of action of the biostimulants on quinoa for drought adaptation. We investigated the impact of two doses of vermicompost (5 and 10 t/ha) and arbuscular mycorrhizal fungi applied individually, or in joint application, on attenuating the negative impacts of water shortage and improving the agro-physiological and biochemical traits of quinoa, as well as soil fertility, under two water regimes (well-watered and drought stress) in open field conditions. Exposure to drought decreased biomass, leaf water potential, and stomatal conductance, and increased malondialdehyde and hydrogen peroxide content. Mycorrhiza and/or vermicompost promoted plant growth by activating photosynthesis machinery and nutrient assimilation, leading to increased total soluble sugars, proteins, and antioxidant enzyme activities in the leaf and root. After the experiment, the soil's total organic matter, phosphorus, nitrogen, calcium, and soil glomalin content improved by the single or combined application of mycorrhiza and vermicompost. This knowledge suggests that the combination of mycorrhiza and vermicompost regulates the physiological and biochemical processes employed by quinoa in coping with drought and improves the understanding of soil-plant interaction.
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Affiliation(s)
- Wissal Benaffari
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Abderrahim Boutasknit
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Mohamed Anli
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Mohamed Ait-El-Mokhtar
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
| | - Youssef Ait-Rahou
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
| | - Raja Ben-Laouane
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
| | - Hela Ben Ahmed
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan;
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan;
- Correspondence: (M.B.); (A.M.); Tel.: +81-252627637 (M.B.); +212-661873158 (A.M.)
| | - Abdelilah Meddich
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
- Correspondence: (M.B.); (A.M.); Tel.: +81-252627637 (M.B.); +212-661873158 (A.M.)
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7
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Malik AA, Bouskill NJ. Drought impacts on microbial trait distribution and feedback to soil carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ashish A. Malik
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
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Reducing Drought Stress in Plants by Encapsulating Plant Growth-Promoting Bacteria with Polysaccharides. Int J Mol Sci 2021; 22:ijms222312979. [PMID: 34884785 PMCID: PMC8657635 DOI: 10.3390/ijms222312979] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 01/02/2023] Open
Abstract
Drought is a major abiotic stress imposed by climate change that affects crop production and soil microbial functions. Plants respond to water deficits at the morphological, biochemical, and physiological levels, and invoke different adaptation mechanisms to tolerate drought stress. Plant growth-promoting bacteria (PGPB) can help to alleviate drought stress in plants through various strategies, including phytohormone production, the solubilization of mineral nutrients, and the production of 1-aminocyclopropane-1-carboxylate deaminase and osmolytes. However, PGPB populations and functions are influenced by adverse soil factors, such as drought. Therefore, maintaining the viability and stability of PGPB applied to arid soils requires that the PGPB have to be protected by suitable coatings. The encapsulation of PGPB is one of the newest and most efficient techniques for protecting beneficial bacteria against unfavorable soil conditions. Coatings made from polysaccharides, such as sodium alginate, chitosan, starch, cellulose, and their derivatives, can absorb and retain substantial amounts of water in the interstitial sites of their structures, thereby promoting bacterial survival and better plant growth.
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9
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Effects of Abiotic Stress on Soil Microbiome. Int J Mol Sci 2021; 22:ijms22169036. [PMID: 34445742 PMCID: PMC8396473 DOI: 10.3390/ijms22169036] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.
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10
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Tan B, Li Y, Liu T, Tan X, He Y, You X, Leong KH, Liu C, Li L. Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:691651. [PMID: 34456936 PMCID: PMC8385539 DOI: 10.3389/fpls.2021.691651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
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Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Tiegang Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yuxin He
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xueji You
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Kah Hon Leong
- Department of Environmental Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- *Correspondence: Chao Liu,
| | - Longguo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- Longguo Li,
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Abstract
The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis. The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.
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Lugo AE. Effects of Extreme Disturbance Events: From Ecesis to Social–Ecological–Technological Systems. Ecosystems 2020. [DOI: 10.1007/s10021-020-00491-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractEcologists addressed the effects of disturbances from the onset of the field by focusing on ecesis, which is the process by which organisms migrate and establish under the environmental conditions created by disturbances. Ecesis is the onset of succession, a self-organizing process whose nature, speed, and outcome depend in part on the outcomes of ecesis and the residual legacies remaining after disturbances. A by-product of succession after a disturbance is the reorganization of species dominance, or novelty. The degree of novelty in the outcome increases with the severity of the disturbance event. Initially, ecologists focused mostly on non-anthropogenic disturbances, but as human activity intensified and became a global force, more attention was given to the effects of anthropogenic disturbances on ecosystems. Today, anthropogenic and non-anthropogenic disturbances and their interactions are increasingly affecting ecosystems, particularly those exposed to extreme disturbance events. Extreme disturbance events are complex and low probability events composed of several disturbance forces that individually and in synergy affect different sectors of ecosystems, including the conditions that drive ecesis. I review the literature on disturbance research including the effects of extreme disturbance events on social–ecological–technological systems (SETSs). A SETS is an ecosystem defined by the flow and accumulation of energy through the medium of organisms, constructed infrastructure, institutions, and their environment. Human intentions, values, and capacities are part of the functioning of SETS, and they can drive ecological processes as do non-anthropogenic forces. Moreover, human-directed activities after an extreme disturbance event affect whole landscapes. The passage of hurricane María over the Puerto Rico SETS established that extreme disturbance events are of such power and complexity that they can influence the level and kind of relationship between humans and the environment, including the structure and species composition of the ecological systems within SETS. However, extreme disturbance events such as hurricanes have not changed the successional trajectory originally impulsed by anthropogenic disturbances. Thus, the species composition and functioning of novel forests in Puerto Rico are tied to economic activity in the social and technological sectors of SETS. It is no longer possible to interpret ecosystem functioning without considering the synergy between anthropogenic and non-anthropogenic extreme disturbances.
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Effects of Nanoparticles on Plant Growth-Promoting Bacteria in Indian Agricultural Soil. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9030140] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Soil bacteria are some of the key players affecting plant productivity. Soil today is exposed to emerging contaminants like metal engineered nanoparticles. The objective of this study was to evaluate the toxicological effects of silver and zinc oxide nanoparticles on bacteria classified as plant growth-promoting bacteria. Three types of bacteria—nitrogen fixers, phosphate solubilizers, and biofilm formers—were exposed to engineered nanoparticles. Initially, the effect of silver and zinc oxide nanoparticles was determined on pure cultures of the bacteria. These nanoparticles were then applied to soil to assess changes in composition of bacterial communities. Impacts of the nanoparticles were analyzed using Illumina MiSeq sequencing of 16S rRNA genes. In the soil used, relative abundances of the dominant and agriculturally significant phyla, namely, Proteobacteria, Actinobacteria, and Firmicutes, were altered in the presence of silver nanoparticles. Silver nanoparticles changed the abundance of the three phyla by 25 to 45%. Zinc oxide nanoparticles showed negligible effects at the phylum level. Thus, silver nanoparticles may impact bacterial communities in soil, and this in turn may influence processes carried out by soil bacteria.
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Bhattacharyya A, Campbell AN, Tfaily MM, Lin Y, Kukkadapu RK, Silver WL, Nico PS, Pett-Ridge J. Redox Fluctuations Control the Coupled Cycling of Iron and Carbon in Tropical Forest Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:14129-14139. [PMID: 30451506 DOI: 10.1021/acs.est.8b03408] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Oscillating redox conditions are a common feature of humid tropical forest soils, driven by an ample supply and dynamics of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. However, the net result of variable soil redox regimes on iron (Fe) mineral dynamics and associated carbon (C) forms and fluxes is poorly understood in tropical soils. Using a 44-day redox incubation experiment with humid tropical forest soils from Puerto Rico, we examined patterns in Fe and C transformations under four redox regimes: static anoxic, "flux 4-day" (4d oxic, 4d anoxic), "flux 8-day" (8d oxic, 4d anoxic) and static oxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides, and led to an increase in soluble Fe(II) and amorphous Fe oxide pools. Preferential dissolution of the less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic C, presumably due to acidification or direct release of organic matter (OM) from dissolving Fe(III) mineral phases. The average nominal oxidation state of water-soluble C was lowest under persistent anoxic conditions, suggesting that more reduced organic compounds were metabolically unavailable for microbial consumption under reducing conditions. Anoxic soil compounds had high H/C values (and were similar to lignin-like compounds) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic C was highest in static oxic soils. These results show how Fe minerals and Fe-OM interactions in tropical soils are highly sensitive to variable redox effects. Shifting soil oxygen availability rapidly impacted exchanges between mineral-sorbed and aqueous C pools, increased the dissolved organic C pool under anoxic conditions implying that the periodicity of low-redox events may control the fate of C in wet tropical soils.
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Affiliation(s)
- Amrita Bhattacharyya
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
| | - Ashley N Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Lin
- Department of Environmental Science, Policy, and Management , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Ravi K Kukkadapu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Peter S Nico
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
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15
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Rodríguez Pérez H, Borrel G, Leroy C, Carrias JF, Corbara B, Srivastava DS, Céréghino R. Simulated drought regimes reveal community resilience and hydrological thresholds for altered decomposition. Oecologia 2018; 187:267-279. [DOI: 10.1007/s00442-018-4123-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/17/2018] [Indexed: 11/28/2022]
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16
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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17
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Srivastava M, Mishra AK. Comparative responses of diazotrophic abundance and community structure to the chemical composition of paddy soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:399-412. [PMID: 29039042 DOI: 10.1007/s11356-017-0375-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0.01) at Chandauli (CHN) as compared to Varanasi (VNS) and Ghazipur (GHJ) districts of Eastern Uttar Pradesh, India, with nitrogenase reductase (nifH) copy number between 1.44 × 103 and 3.34 × 103 copy g-1 soil. Fourier-transform infrared (FT-IR) spectroscopy data identified -CO-, C=O ([Formula: see text] and -NH-), [Formula: see text], and OH- as dominant organic functional groups in the paddy soil. Multivariate analysis was performed to get a clear and more accurate picture of interactions between free-living diazotrophs and abiotic soil factors. Regression analysis suggested a similar trend of distribution of different functional groups along each site. Relative abundance and diversity of diazotrophic population increased in response to FT-IR-based soil organic fractions. Maximum number of FT-IR spectral peak at sites in the Chandauli district augmented its bacterial diazotrophic diversity and abundance. Taken together, the present study sheds light on the substrate-driven composition of the microbial population of selected paddy areas.
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Affiliation(s)
- Meenakshi Srivastava
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
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18
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Smith AP, Bond-Lamberty B, Benscoter BW, Tfaily MM, Hinkle CR, Liu C, Bailey VL. Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nat Commun 2017; 8:1335. [PMID: 29109458 PMCID: PMC5673896 DOI: 10.1038/s41467-017-01320-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/11/2017] [Indexed: 11/20/2022] Open
Abstract
Droughts and other extreme precipitation events are predicted to increase in intensity, duration, and extent, with uncertain implications for terrestrial carbon (C) sequestration. Soil wetting from above (precipitation) results in a characteristically different pattern of pore-filling than wetting from below (groundwater), with larger, well-connected pores filling before finer pore spaces, unlike groundwater rise in which capillary forces saturate the finest pores first. Here we demonstrate that pore-scale wetting patterns interact with antecedent soil moisture conditions to alter pore-scale, core-scale, and field-scale C dynamics. Drought legacy and wetting direction are perhaps more important determinants of short-term C mineralization than current soil moisture content in these soils. Our results highlight that microbial access to C is not solely limited by physical protection, but also by drought or wetting-induced shifts in hydrologic connectivity. We argue that models should treat soil moisture within a three-dimensional framework emphasizing hydrologic conduits for C and resource diffusion. The impacts of top down (precipitation) and bottom-up (groundwater rise) wetting processes on carbon sequestration are poorly understood. Here, the authors use incubation experiments to show that drought legacy and pore-scale wetting patterns are important factors controlling short-term carbon dynamics.
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Affiliation(s)
- A Peyton Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
| | - Ben Bond-Lamberty
- Joint Global Change Research Institute, Pacific Northwest National Laboratory, 5825 University Research Court, Suite 3500, College Park, MD, 20740, USA
| | - Brian W Benscoter
- Florida Atlantic University, Department of Biological Sciences, 3200 College Avenue, Davie, FL, 33314, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - C Ross Hinkle
- University of Central Florida, Ecosystem Processes and Services Laboratory, 4110 Libra Drive, Orlando, FL, 3216, USA
| | - Chongxuan Liu
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA.,Southern University of Science and Technology, School of Environmental Science and Engineering, 518055, Shenzhen, China
| | - Vanessa L Bailey
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
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19
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Hydrological legacy determines the type of enzyme inhibition in a peatlands chronosequence. Sci Rep 2017; 7:9948. [PMID: 28855607 PMCID: PMC5577268 DOI: 10.1038/s41598-017-10430-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 08/08/2017] [Indexed: 11/08/2022] Open
Abstract
Peatland ecosystems contain one-third of the world’s soil carbon store and many have been exposed to drought leading to a loss of carbon. Understanding biogeochemical mechanisms affecting decomposition in peatlands is essential for improving resilience of ecosystem function to predicted climate change. We investigated biogeochemical changes along a chronosequence of hydrological restoration (dry eroded gully, drain-blocked <2 years, drain blocked <7 years and wet pristine site), and examined whether hydrological legacy alters the response of β-glucosidase kinetics (i.e. type of inhibition) to short-term drying and waterlogging. In the dry eroded gully at depth, low phenolic concentrations were associated with enhanced β-glucosidase enzyme activities (Vmax) but short-term drying and waterlogging caused a significant increase of dissolved organic carbon (DOC) and phenolics associated with increases in Vmax (enzyme production) and Km (indicative of competitive inhibition). Inhibition within the drain blocked and pristine sites at depth exhibited non-competitive inhibition (decreased Vmax), whilst uncompetitive inhibition (decreased Vmax and Km) occurred in surface peat explained by variation in humic substances and phenolics. These results suggest that loss of carbon by short-term drought or rewetting may occur from sites with a legacy of drought due to the release of non-inhibitory phenolics that permits enhanced enzyme activity.
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20
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Nicolás C, Almeida JP, Ellström M, Bahr A, Bone SE, Rosenstock NP, Bargar JR, Tunlid A, Persson P, Wallander H. Chemical changes in organic matter after fungal colonization in a nitrogen fertilized and unfertilized Norway spruce forest. PLANT AND SOIL 2017; 419:113-126. [PMID: 32009679 PMCID: PMC6959379 DOI: 10.1007/s11104-017-3324-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/22/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Decomposition and transformation of organic matter (OM) in forest soils are conducted by the concomitant action of saprotrophic and mycorrhizal fungi. Here, we examine chemical changes in OM after fungal colonization in nitrogen fertilized and unfertilized soils from a Norway spruce forest. METHODS Sand-filled bags amended with composted maize leaves were placed in the forest soil and harvested after 17 months. Infrared and near edge X-ray absorption fine structure spectroscopies were used to study the chemical changes in the OM. Fungal community composition of the bags was also evaluated. RESULTS The proportion of ectomycorrhizal fungi declined in the fertilized plots, but the overall fungal community composition was similar between N treatments. Decomposition of the OM was, independently of the N level or soil horizon, accompanied by an increase of C/N ratio of the mesh-bag content. Moreover, the proportions of carboxylic compounds in the incubated OM increased in the mineral horizon, while heterocyclic-N compounds decreased, especially in unfertilized plots with higher N demand from the trees. CONCLUSIONS Our results indicate that more oxidized organic C and less heterocyclic-N proportions in the OM remain after fungal colonization in the mineral layers, and suggest that ectomycorrhizal fungi transfer less heterocyclic-N from the mesh bags to the host trees under high N levels.
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Affiliation(s)
- César Nicolás
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Department of Biology, Ecology Building, Lund University, SE 22362 Lund, Sweden
| | - Juan P. Almeida
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Magnus Ellström
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Adam Bahr
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Sharon E. Bone
- Chemistry and Catalysis Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Nicholas P. Rosenstock
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - John R. Bargar
- Chemistry and Catalysis Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Per Persson
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Håkan Wallander
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
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21
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Naylor D, Coleman-Derr D. Drought Stress and Root-Associated Bacterial Communities. FRONTIERS IN PLANT SCIENCE 2017; 8:2223. [PMID: 29375600 PMCID: PMC5767233 DOI: 10.3389/fpls.2017.02223] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/18/2017] [Indexed: 05/20/2023]
Abstract
Root-associated bacterial communities play a vital role in maintaining health of the plant host. These communities exist in complex relationships, where composition and abundance of community members is dependent on a number of factors such as local soil chemistry, plant genotype and phenotype, and perturbations in the surrounding abiotic environment. One common perturbation, drought, has been shown to have drastic effects on bacterial communities, yet little is understood about the underlying causes behind observed shifts in microbial abundance. As drought may affect root bacterial communities both directly by modulating moisture availability, as well as indirectly by altering soil chemistry and plant phenotypes, we provide a synthesis of observed trends in recent studies and discuss possible directions for future research that we hope will provide for more knowledgeable predictions about community responses to future drought events.
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Affiliation(s)
- Dan Naylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
- *Correspondence: Devin Coleman-Derr,
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Kivlin SN, Hawkes CV. Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest. PLoS One 2016; 11:e0159131. [PMID: 27391450 PMCID: PMC4938164 DOI: 10.1371/journal.pone.0159131] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/28/2016] [Indexed: 11/18/2022] Open
Abstract
The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.
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Affiliation(s)
- Stephanie N Kivlin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, United States of America
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, United States of America
- * E-mail:
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