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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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Bech TB, Badawi N, Rosenbom AE. Impact of surface-applied liquid manure on the drainage resistance profile of an agricultural tile-drained clay till field. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:656-669. [PMID: 35435263 DOI: 10.1002/jeq2.20354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Dissemination of antibiotic resistance genes (ARGs) in aquatic environments is a concern due to human and animal health. Application of liquid manure on agricultural land is an important source of ARGs, where pathogens, antibiotic-resistant bacteria, and selective agents are released. To improve our understanding of ARGs spreading through soils, our main objective was to evaluate the effectiveness of the soil as a barrier protecting water resources. Over the course of a year, profiles and abundances of ARGs and mobile genetic elements in soil and drainage from an agricultural tile-drained clay till field were investigated upon liquid pig manure application by applying high-throughput quantitative polymerase chain reaction targeting 143 genes. The findings were as follows: (a) 97 genes were detected, where only the transposon gene tnpA-03/ IS6 was shared between the genes detected in drainage and those in acidified liquid manure or fertilized soils, indicating that liquid manure application had a limited impact on the drainage resistance profile; (b) intI1 gene was present in ∼60% of drainage samples in concentrations up to 1,634 intI1 ml-1 ; and (c) evapotranspiration from barley (Hordeum vulgare L., 'KWS Irina') and a low groundwater table appeared to reduce preferential transport to drainage during the first 3 mo of liquid manure application. Interestingly, the first preferential transport to drainage was observed immediately after the harvest of spring barley. Overall, during the monitoring year we found the soil to be an effective barrier against the spread of fecal ARGs even though the occurrence of the intI1 gene questions the barrier effect from previous years.
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Affiliation(s)
- Tina B Bech
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Nora Badawi
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Annette E Rosenbom
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
- Rambøll Danmark A/S, Hannemanns Allé 53, 2300 Copenhagen S, Copenhagen, Denmark
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Lutterodt G, Miyittah MK, Addy B, Ansa ED, Takase M. Groundwater pollution assessment in a coastal aquifer in Cape Coast, Ghana. Heliyon 2021; 7:e06751. [PMID: 33948506 PMCID: PMC8080048 DOI: 10.1016/j.heliyon.2021.e06751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 04/05/2021] [Indexed: 12/17/2022] Open
Abstract
This work presents an assessment of the chemico-physical and microbial quality of water samples from hand-dug wells in the shallow aquifer of three communities neighbouring the University of Cape Coast, Ghana. Sanitary risk inspection was undertaken at each well location and the physical parameters including electrical conductivity, pH, Dissolved Oxygen (DO) and etc. were measured in situ via probes. Microbial groundwater quality was analysed using membrane filtration method. Samples of water were analysed for the pollution indicator anions including chloride and nitrate. In addition, the possible persistence of bacteria in groundwater environments in the absence of predator organisms were studied and results fitted with exponential, second-order polynomial and linear distribution models. Sanitary risk inspection and microbial quality results indicate that all the wells were at risk and polluted with total coliforms from on-site sanitation. Twenty-five percent (7 out of 28) of the wells recorded DO concentration within acceptable limits of drinking water standards (> 5 mg/L). Average chloride concentration, 360.5 mg/L (range: 46 mg/L to 844 mg/L) and average electrical conductivity value of 1.5 mS/cm (range: 213 μS/cm to 2.7 mS/cm) were both higher than WHO recommended limits. Acidic conditions (pH < 6.5) were observed in water samples, indicating mineralisation of the aquifer. The high EC values and chloride content in groundwater were attributable to dry atmospheric aerosol deposition and possible mineral dissolution in the aquifer. Bacteria re-growth experiment results indicate that second-order polynomial distribution best describes bacteria inactivation rates in the absence of antagonist predators in our work. Extrapolation of time for complete inactivation of bacteria under groundwater environment ranged from 0.1 to 4 years indicating bacteria can persist in aquifers for long period of time. It was concluded that all the wells are at risk of pollution and polluted with faecal matter and atmospheric aerosols.
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Affiliation(s)
- George Lutterodt
- Water Resources Development Department, University of Environment and Sustainable Development, PMB Somanya, Ghana
| | | | - Bright Addy
- School of Pharmacy, Central University, Miotso
| | | | - Mohammed Takase
- Environmental Science Department, University of Cape Coast, Ghana
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The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA. Appl Environ Microbiol 2021; 87:AEM.02673-20. [PMID: 33310710 PMCID: PMC7851703 DOI: 10.1128/aem.02673-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.
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Thorup-Kristensen K, Halberg N, Nicolaisen M, Olesen JE, Crews TE, Hinsinger P, Kirkegaard J, Pierret A, Dresbøll DB. Digging Deeper for Agricultural Resources, the Value of Deep Rooting. TRENDS IN PLANT SCIENCE 2020; 25:406-417. [PMID: 31964602 DOI: 10.1016/j.tplants.2019.12.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 05/25/2023]
Abstract
In the quest for sustainable intensification of crop production, we discuss the option of extending the root depth of crops to increase the volume of soil exploited by their root systems. We discuss the evidence that deeper rooting can be obtained by appropriate choice of crop species, by plant breeding, or crop management and its potential contributions to production and sustainable development goals. Many studies highlight the potentials of deeper rooting, but we evaluate its contributions to sustainable intensification of crop production, the causes of the limited research into deep rooting of crops, and the research priorities to fill the knowledge gaps.
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Affiliation(s)
- Kristian Thorup-Kristensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
| | - Niels Halberg
- DCA - Danish Centre for Food and Agriculture, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | - Mette Nicolaisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus Universitet, Blichers Allé 20, 8830 Tjele, Denmark
| | - Timothy E Crews
- The Land Institute, 2440E Water Well Rd. Salina, KS 67401, USA
| | - Philippe Hinsinger
- Eco&Sols, University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - John Kirkegaard
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Alain Pierret
- Institut d'Écologie et des Sciences de l'Environnement de Paris (iEES-Paris), Sorbonne Université, CNRS, INRAE, IRD, Université de Paris, Université Paris Est Creteil, Paris, France; Department of Agricultural Land Management (DALaM), Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - Dorte Bodin Dresbøll
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Pennanen T, Fritze H, de Boer W, Baldrian P. Editorial: special issue on the ecology of soil microorganisms. FEMS Microbiol Ecol 2019; 95:5628114. [PMID: 31738407 DOI: 10.1093/femsec/fiz154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Hannu Fritze
- Natural Resources Institute Finland (Luke), Helsinki
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Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile. Appl Environ Microbiol 2019; 85:AEM.02658-18. [PMID: 30658975 PMCID: PMC6414393 DOI: 10.1128/aem.02658-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 11/29/2022] Open
Abstract
The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats. This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (−3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of −6.3 to −8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea. Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment. IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.
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