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Storkey J, Maclaren C, Bullock JM, Norton LR, Redhead JW, Pywell RF. Quantifying farm sustainability through the lens of ecological theory. Biol Rev Camb Philos Soc 2024; 99:1700-1716. [PMID: 38695217 DOI: 10.1111/brv.13088] [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: 08/09/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 09/03/2024]
Abstract
The achievements of the Green Revolution in meeting the nutritional needs of a growing global population have been won at the expense of unintended consequences for the environment. Some of these negative impacts are now threatening the sustainability of food production through the loss of pollinators and natural enemies of crop pests, the evolution of pesticide resistance, declining soil health and vulnerability to climate change. In the search for farming systems that are sustainable both agronomically and environmentally, alternative approaches have been proposed variously called 'agroecological', 'conservation agriculture', 'regenerative' and 'sustainable intensification'. While the widespread recognition of the need for more sustainable farming is to be welcomed, this has created etymological confusion that has the potential to become a barrier to transformation. There is a need, therefore, for objective criteria to evaluate alternative farming systems and to quantify farm sustainability against multiple outcomes. To help meet this challenge, we reviewed the ecological theories that explain variance in regulating and supporting ecosystem services delivered by biological communities in farmland to identify guiding principles for management change. For each theory, we identified associated system metrics that could be used as proxies for agroecosystem function. We identified five principles derived from ecological theory: (i) provide key habitats for ecosystem service providers; (ii) increase crop and non-crop habitat diversity; (iii) increase edge density: (iv) increase nutrient-use efficiency; and (v) avoid extremes of disturbance. By making published knowledge the foundation of the choice of associated metrics, our aim was to establish a broad consensus for their use in sustainability assessment frameworks. Further analysis of their association with farm-scale data on biological communities and/or ecosystem service delivery would provide additional validation for their selection and support for the underpinning theories.
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Affiliation(s)
- Jonathan Storkey
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Chloe Maclaren
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Almas Alle 8, Uppsala, 750 07, Sweden
| | - James M Bullock
- UK Centre for Ecology & Hydrology (UKCEH), Maclean Building, Benson Lane, Wallingford, OX10 8BB, UK
| | - Lisa R Norton
- UKCEH, Lancaster Environment Centre, Lancaster, LA1 4AP, UK
| | - John W Redhead
- UK Centre for Ecology & Hydrology (UKCEH), Maclean Building, Benson Lane, Wallingford, OX10 8BB, UK
| | - Richard F Pywell
- UK Centre for Ecology & Hydrology (UKCEH), Maclean Building, Benson Lane, Wallingford, OX10 8BB, UK
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2
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Gupta VVSR, Tiedje JM. Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales. MLIFE 2024; 3:21-41. [PMID: 38827504 PMCID: PMC11139212 DOI: 10.1002/mlf2.12116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 06/04/2024]
Abstract
The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.
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Affiliation(s)
| | - James M. Tiedje
- Centre for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
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3
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Rotchell JM, Mendrik F, Chapman E, Flintoft P, Panter I, Gallio G, McDonnell C, Liddle CR, Jennings D, Schofield J. The contamination of in situ archaeological remains: A pilot analysis of microplastics in sediment samples using μFTIR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169941. [PMID: 38199369 DOI: 10.1016/j.scitotenv.2024.169941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND Microplastics (MPs) are found in all environments: aquatic, airborne, and terrestrial. While their presence is not disputed, their potential impacts are not yet known. OBJECTIVE To undertake a pilot analysis of MP contamination in archaeological sediment samples, taken in the late 1980s from two archaeological excavation sites in the historic city of York (UK) as well as contemporary sources close to the same sites, with respect to the presence (if any), levels, and characteristics of any particles identified. METHODS This study analysed pre-digested sediment samples as follows: n = 3 from Queens Hotel (QH) site and n = 3 Wellington Row (WR) contemporary core-source, and n = 3 QH and n = 3 WR archival-source samples, alongside procedural controls (n = 8), using μFTIR spectroscopy (size limitation of 5 μm) to detect and characterise any MPs present. RESULTS In total, 66 MP particles consisting of 16 MP polymer types were identified across both site and contemporary/archived samples. The highest levels of MP particles, 20,588 MP/kg was identified at the lowest sample depth (∼7.35 m) at archived WR, 5910 MP/kg in the mid depth layer (∼5.85 m) at the contemporary QH site. Of the MPs detected in sediment samples overall, polytetrafluoroethylene (PTFE), polybutylene sulfone (PSU), and polypropylene: polyethylene (PE:PP) copolymer polymer types were most abundant; mainly fragmented and irregular shape. CONCLUSIONS This is believed to be the first evidence of MP contamination in archaeological sediment (or soil) samples with polymers and size ranges measured and while accounting for procedural blanks. These results support the phenomenon of transport of MPs within archaeological stratigraphy, and the characterisation of types, shapes and size ranges identified therein. Through contamination, MPs may compromise the scientific value of archaeological deposits, and environmental proxies suspended within significant sediment, and as such represent a new consideration in the dynamism of, as well as arguments for preserving, archaeological deposits in situ.
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Affiliation(s)
- Jeanette M Rotchell
- School of Natural Sciences, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom; College of Health and Science, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom.
| | - Freija Mendrik
- School of Natural Sciences, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom; Energy and Environment Institute, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom
| | - Emma Chapman
- School of Natural Sciences, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom
| | - Paul Flintoft
- York Archaeology, (York), 47 Aldwark, York, North Yorkshire YO1 7BX, United Kingdom
| | - Ian Panter
- York Archaeology, (York), 47 Aldwark, York, North Yorkshire YO1 7BX, United Kingdom
| | - Giulia Gallio
- York Archaeology, (York), 47 Aldwark, York, North Yorkshire YO1 7BX, United Kingdom
| | - Christine McDonnell
- School of Natural Sciences, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom
| | - Catriona R Liddle
- School of Natural Sciences, University of Hull, Kingston-upon-Hull HU6 7RX, United Kingdom
| | - David Jennings
- York Archaeology, (York), 47 Aldwark, York, North Yorkshire YO1 7BX, United Kingdom
| | - John Schofield
- Department of Archaeology, University of York, King's Manor, Exhibition Square, York YO17EP, United Kingdom
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4
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LeBlanc NR, Harrigian FC. Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil. MICROBIAL ECOLOGY 2024; 87:44. [PMID: 38367043 PMCID: PMC10874327 DOI: 10.1007/s00248-024-02361-8] [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: 10/20/2023] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.
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Affiliation(s)
- Nicholas R LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA.
| | - Fiona C Harrigian
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA
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5
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Rutkowska N, Drożdżyński P, Ryngajłło M, Marchut-Mikołajczyk O. Plants as the Extended Phenotype of Endophytes-The Actual Source of Bioactive Compounds. Int J Mol Sci 2023; 24:10096. [PMID: 37373241 DOI: 10.3390/ijms241210096] [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: 05/19/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes.
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Affiliation(s)
- Natalia Rutkowska
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Piotr Drożdżyński
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Olga Marchut-Mikołajczyk
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
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6
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Manzano P, Rowntree J, Thompson L, del Prado A, Ederer P, Windisch W, Lee MRF. Challenges for the balanced attribution of livestock's environmental impacts: the art of conveying simple messages around complex realities. Anim Front 2023; 13:35-44. [PMID: 39105191 PMCID: PMC11299730 DOI: 10.1093/af/vfac096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024] Open
Affiliation(s)
- Pablo Manzano
- Basque Centre for Climate Change (BC3), E-48940
Leioa, Spain
- Ikerbasque — Basque Foundation of Science, E-48007
Bilbao, Spain
| | - Jason Rowntree
- Department of Animal Science, Michigan State University,
East Lansing, MI, USA
| | - Logan Thompson
- Department of Animal Sciences and Industry, Kansas State
University, Manhattan, KS, USA
| | - Agustín del Prado
- Basque Centre for Climate Change (BC3), E-48940
Leioa, Spain
- Ikerbasque — Basque Foundation of Science, E-48007
Bilbao, Spain
| | - Peer Ederer
- Global Food and Agriculture Network,
Rapperswil, Switzerland
| | - Wilhelm Windisch
- Technical University of Munich, Liesel Beckmann
Straße 2, D-85354 Freising, Germany
| | - Michael R F Lee
- School of Sustainable Food and Farming, Harper Adams
University, Edgmond, Newport, Shropshire, TF10
8NB, UK
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7
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Zhao B, Yang Y, Zhao C, Zhang C, Zhang Z, Wang L, Wang S, Wang J. Exploration of the metabolic flexibility of glycogen accumulating organisms through metatranscriptome analysis and metabolic characterization. J Environ Sci (China) 2023; 126:234-248. [PMID: 36503752 DOI: 10.1016/j.jes.2022.05.012] [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: 02/24/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 06/17/2023]
Abstract
Glycogen accumulating organisms (GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds supernatant of a reactor were decanted following the anaerobic period to enrich GAOs. Long-term monitoring demonstrated that the system was stable and exhibited typical characteristics of GAOs metabolism. Acetate was completely consumed after 60 min of the anaerobic phase. The level of glycogen decreased from 0.20 to 0.14 g/gSS during the anaerobic phase, whereas the level of glycogen significantly increased to 0.21g/gSS at the end of the aerobic period. Moreover, there was almost no phosphate release and absorption in the complete periods, thus confirming the successful construction of a GAOs enrichment system. Microbial community analysis demonstrated that Ca. Contendobacter was among the core functional genera and showed the highest activity among all of the communities. Furthermore, our study is the first to identify the involvement of the ethyl-malonyl-CoA pathway in the synthesis of polyhydroxyvalerate via croR, ccr, ecm, mcd, mch and mcl genes. The Embden-Meyerhof-Parnas (EMP) pathway was preferentially used via glgP. Furthermore, the glyoxylate cycle was the main source of ATP under anaerobic conditions, whereas the tricarboxylic acid cycle provided ATP under aerobic conditions. aceA and mdh appeared to be major modulators of the glyoxylate pathway for controlling energy flow. Collectively, our findings not only revealed the crucial metabolic mechanisms in a GAOs enrichment system but also provided insights into the potential application of Ca. Contendobacter for wastewater treatment.
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Affiliation(s)
- Bin Zhao
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Yanping Yang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China; Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Chunchun Zhang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China; Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Zhaohui Zhang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Liang Wang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China.
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8
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Bickel S, Or D. Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria. Commun Biol 2023; 6:322. [PMID: 36966207 PMCID: PMC10039866 DOI: 10.1038/s42003-023-04703-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Earth's diverse soil microbiomes host bacteria within dynamic and fragmented aqueous habitats that occupy complex pore spaces and restrict the spatial range of ecological interactions. Yet, the spatial distributions of bacterial cells in soil communities remain underexplored. Here, we propose a modelling framework representing submillimeter-scale distributions of soil bacteria based on physical constraints supported by individual-based model results and direct observations. The spatial distribution of bacterial cell clusters modulates various metabolic interactions and soil microbiome functioning. Dry soils with long diffusion times limit localized interactions of the sparse communities. Frequently wet soils enable long-range trophic interactions between dense cell clusters through connected aqueous pathways. Biomes with high carbon inputs promote large and dense cell clusters where anoxic microsites form even in aerated soils. Micro-geographic considerations of difficult-to-observe microbial processes can improve the interpretation of data from bulk soil samples.
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Affiliation(s)
- Samuel Bickel
- ETH Zurich, Zürich, 8092, Switzerland.
- Graz University of Technology, Graz, 8010, Austria.
| | - Dani Or
- ETH Zurich, Zürich, 8092, Switzerland
- Desert Research Institute, Reno, NV, USA
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9
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Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition. Int J Mol Sci 2023; 24:ijms24010872. [PMID: 36614337 PMCID: PMC9821613 DOI: 10.3390/ijms24010872] [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: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
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10
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Neal AL, Barrat HA, Bacq-Lebreuil A, Qin Y, Zhang X, Takahashi T, Rubio V, Hughes D, Clark IM, Cárdenas LM, Gardiner LJ, Krishna R, Glendining ML, Ritz K, Mooney SJ, Crawford JW. Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype. NATURE FOOD 2023; 4:51-60. [PMID: 37118575 DOI: 10.1038/s43016-022-00671-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/14/2022] [Indexed: 04/30/2023]
Abstract
Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.
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Affiliation(s)
- Andrew L Neal
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK.
| | - Harry A Barrat
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- The Carbon Trust, London, UK
| | - Aurélie Bacq-Lebreuil
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
- Genesis, Lisors, France
| | - Yuwei Qin
- Department of Environmental Sciences, Wageningen University, Wageningen, The Netherlands
| | - Xiaoxian Zhang
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Taro Takahashi
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- Bristol Veterinary School, University of Bristol, Langford, UK
| | - Valentina Rubio
- Programa de Producción y Sustentabilidad Ambiental, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - David Hughes
- Intelligent Data Ecosystems, Rothamsted Research, Harpenden, UK
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Laura M Cárdenas
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
| | | | - Ritesh Krishna
- IBM Research Europe - Daresbury, The Hartree Centre, Warrington, UK
| | | | - Karl Ritz
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - Sacha J Mooney
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - John W Crawford
- Adam Smith Business School, University of Glasgow, Glasgow, UK
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11
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Vidiella B, Solé R. Ecological firewalls for synthetic biology. iScience 2022; 25:104658. [PMID: 35832885 PMCID: PMC9272386 DOI: 10.1016/j.isci.2022.104658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while-when required-preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined.
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Affiliation(s)
- Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Cerdanyola del Valles, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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12
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Zhang X, Whalley PA, Gregory AS, Whalley WR, Coleman K, Neal AL, Mooney SJ, Soga K, Illangasekare TH. An overlooked mechanism underlying the attenuated temperature response of soil heterotrophic respiration. J R Soc Interface 2022; 19:20220276. [PMID: 35855594 PMCID: PMC9297011 DOI: 10.1098/rsif.2022.0276] [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] [Indexed: 02/02/2023] Open
Abstract
Biogeochemical reactions occurring in soil pore space underpin gaseous emissions measured at macroscopic scales but are difficult to quantify due to their complexity and heterogeneity. We develop a volumetric-average method to calculate aerobic respiration rates analytically from soil with microscopic soil structure represented explicitly. Soil water content in the model is the result of the volumetric-average of the microscopic processes, and it is nonlinearly coupled with temperature and other factors. Since many biogeochemical reactions are driven by oxygen (O2) which must overcome various resistances before reaching reactive microsites from the atmosphere, the volumetric-average results in negative feedback between temperature and soil respiration, with the magnitude of the feedback increasing with soil water content and substrate quality. Comparisons with various experiments show the model reproduces the variation of carbon dioxide emission from soils under different water content and temperature gradients, indicating that it captures the key microscopic processes underpinning soil respiration. We show that alongside thermal microbial adaptation, substrate heterogeneity and microbial turnover and carbon use efficiency, O2 dissolution and diffusion in water associated with soil pore space is another key explanation for the attenuated temperature response of soil respiration and should be considered in developing soil organic carbon models.
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Affiliation(s)
- Xiaoxian Zhang
- Sustainable Soils and Crops, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Peter A. Whalley
- School of Mathematics, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew S. Gregory
- Sustainable Soils and Crops, Rothamsted Research, Harpenden AL5 2JQ, UK
| | | | - Kevin Coleman
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke EX20 2SB, UK
| | - Andrew L. Neal
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke EX20 2SB, UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Kenichi Soga
- Department of Civil and Environmental Engineering, University of California–Berkeley, Berkeley, CA 94720, USA
| | - Tissa H. Illangasekare
- Centre for Experimental Study of Subsurface Environmental Processes, Colorado School of Mines, Golden, CO, USA
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13
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Animal board invited review: Animal source foods in healthy, sustainable, and ethical diets - An argument against drastic limitation of livestock in the food system. Animal 2022; 16:100457. [PMID: 35158307 DOI: 10.1016/j.animal.2022.100457] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Animal source foods are evolutionarily appropriate foods for humans. It is therefore remarkable that they are now presented by some as unhealthy, unsustainable, and unethical, particularly in the urban West. The benefits of consuming them are nonetheless substantial, as they offer a wide spectrum of nutrients that are needed for cell and tissue development, function, and survival. They play a role in proper physical and cognitive development of infants, children, and adolescents, and help promote maintenance of physical function with ageing. While high-red meat consumption in the West is associated with several forms of chronic disease, these associations remain uncertain in other cultural contexts or when consumption is part of wholesome diets. Besides health concerns, there is also widespread anxiety about the environmental impacts of animal source foods. Although several production methods are detrimental (intensive cropping for feed, overgrazing, deforestation, water pollution, etc.) and require substantial mitigation, damaging impacts are not intrinsic to animal husbandry. When well-managed, livestock farming contributes to ecosystem management and soil health, while delivering high-quality foodstuffs through the upcycling of resources that are otherwise non-suitable for food production, making use of marginal land and inedible materials (forage, by-products, etc.), integrating livestock and crop farming where possible has the potential to benefit plant food production through enhanced nutrient recycling, while minimising external input needs such as fertilisers and pesticides. Moreover, the impacts on land use, water wastage, and greenhouse gas emissions are highly contextual, and their estimation is often erroneous due to a reductionist use of metrics. Similarly, whether animal husbandry is ethical or not depends on practical specificities, not on the fact that animals are involved. Such discussions also need to factor in that animal husbandry plays an important role in culture, societal well-being, food security, and the provision of livelihoods. We seize this opportunity to argue for less preconceived assumptions about alleged effects of animal source foods on the health of the planet and the humans and animals involved, for less top-down planning based on isolated metrics or (Western) technocratic perspectives, and for more holistic and circumstantial approaches to the food system.
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14
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Corenblit D, Corbara B, Steiger J. Biogeomorphological eco-evolutionary feedback between life and geomorphology: a theoretical framework using fossorial mammals. Naturwissenschaften 2021; 108:55. [PMID: 34661745 DOI: 10.1007/s00114-021-01760-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 12/20/2022]
Abstract
Engineer organisms not only adapt to pre-existing environmental conditions but also co-construct their physical environment. By doing so, they can subsequently change selection pressures for themselves and other species, as well as change community and ecosystem structures and functions. Focusing on one representative example, i.e., fossorial mammals, we show that geomorphological Earth system components are crucial for understanding and quantifying links between evolutionary and ecosystem dynamics and that feedbacks between geomorphology and engineer organisms constitute a major driver of geomorphological organization on the Earth's surface. We propose a biogeomorphological eco-evolutionary feedback synthesis from the gene to the landscape where eco-evolutionary feedbacks are mediated by the geomorphological dimensions of a niche that are affected by engineer organisms, such as fossorial mammals. Our concept encompasses (i) the initial responses of fossorial mammals to environmental constraints that enhance the evolution of their morphological and biomechanical traits for digging in the soil; (ii) specific adaptations of engineer fossorial mammals (morphological, biomechanical, physiological and behavioural feedback traits for living in burrows) to their constructed geomorphological environment; and (iii) ecological and evolutionary feedbacks diffusing at the community and ecological levels. Such a new perspective in geomorphology may lead to a better conceptualization and analysis of Earth surface processes and landforms as parts of complex adaptive systems in which Darwinian selection processes at lower landscape levels lead to self-organization of higher-level landforms and landscapes.
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Affiliation(s)
- Dov Corenblit
- Université Clermont Auvergne, CNRS, GEOLAB, 63000, Clermont-Ferrand, France.
- Université de Toulouse, CNRS, Laboratoire Écologie Fonctionnelle et Environnement, 31062, Toulouse, France.
| | - Bruno Corbara
- Université Clermont Auvergne, CNRS, LMGE, 63000, Clermont-Ferrand, France
| | - Johannes Steiger
- Université Clermont Auvergne, CNRS, GEOLAB, 63000, Clermont-Ferrand, France
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15
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George PBL, Fidler DB, Van Nostrand JD, Atkinson JA, Mooney SJ, Creer S, Griffiths RI, McDonald JE, Robinson DA, Jones DL. Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation. Front Microbiol 2021; 12:735022. [PMID: 34594317 PMCID: PMC8477002 DOI: 10.3389/fmicb.2021.735022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/09/2021] [Indexed: 01/16/2023] Open
Abstract
Soil organic matter is composed of a variety of carbon (C) forms. However, not all forms are equally accessible to soil microorganisms. Deprivation of C inputs will cause changes in the physical and microbial community structures of soils; yet the trajectories of such changes are not clear. We assessed microbial communities using phospholipid fatty acid profiling, metabarcoding, CO2 emissions, and functional gene microarrays in a decade-long C deprivation field experiment. We also assessed changes in a range of soil physicochemical properties, including using X-ray Computed Tomography imaging to assess differences in soil structure. Two sets of soils were deprived of C inputs by removing plant inputs for 10 years and 1 year, respectively. We found a reduction in diversity measures, after 10 years of C deprivation, which was unexpected based on previous research. Fungi appeared to be most impacted, likely due to competition for scarce resources after exhausting the available plant material. This suggestion was supported by evidence of bioindicator taxa in non-vegetated soils that may directly compete with or consume fungi. There was also a reduction in copies of most functional genes after 10 years of C deprivation, though gene copies increased for phytase and some genes involved in decomposing recalcitrant C and methanogenesis. Additionally, soils under C deprivation displayed expected reductions in pH, organic C, nitrogen, and biomass as well as reduced mean pore size, especially in larger pores. However, pore connectivity increased after 10 years of C deprivation contrary to expectations. Our results highlight concurrent collapse of soil structure and biodiversity following long-term C deprivation. Overall, this study shows the negative trajectory of continuous C deprivation and loss of organic matter on a wide range of soil quality indicators and microorganisms.
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Affiliation(s)
- Paul B L George
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,UK Centre for Ecology & Hydrology, Bangor, United Kingdom.,Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
| | - David B Fidler
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, United States
| | - Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, United Kingdom
| | - Sacha J Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, United Kingdom
| | - Simon Creer
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | - James E McDonald
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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16
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Neal AL, Hughes D, Clark IM, Jansson JK, Hirsch PR. Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity. mSystems 2021; 6:e0105620. [PMID: 34042469 PMCID: PMC8269249 DOI: 10.1128/msystems.01056-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/29/2021] [Indexed: 11/20/2022] Open
Abstract
How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity-here based on microbial small subunit rRNA gene phylotypes-does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately. IMPORTANCE Changes in soil microbiome diversity and function brought about by land management are predicted to influence a range of environmental services provided by soil, including provision of food and clean water. However, opportunities to compare the long-term effects of combinations of stresses imposed by different management approaches are limited. We exploit a globally unique 50-year field experiment, demonstrating that soil management practices alter microbiome diversity, community traits, and assembly. Grassland soil microbiomes are dominated by fewer-but phylogenetically more diverse-prokaryote phylotypes which sustain larger genomes than microbiomes in arable or bare fallow soil maintained free of plants. Dominant fungi in grassland soils are less phylogenetically diverse than those in arable or fallow soils. Soil tillage increases stochastic processes in microbiome assembly: this, combined with reduced plant biomass, presents opportunities for organisms with a capacity for pathogenesis to become established in stressed soils.
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Affiliation(s)
- Andrew L. Neal
- Department of Sustainable Agriculture Science, Rothamsted Research, North Wyke, Devon, United Kingdom
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian M. Clark
- Department of Sustainable Agriculture Science, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Penny R. Hirsch
- Department of Sustainable Agriculture Science, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
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17
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Survey of artificial intelligence approaches in the study of anthropogenic impacts on symbiotic organisms – a holistic view. Symbiosis 2021. [DOI: 10.1007/s13199-021-00778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Garaycochea S, Romero H, Beyhaut E, Neal AL, Altier N. Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities. FEMS Microbiol Ecol 2021; 96:5920615. [PMID: 33038219 DOI: 10.1093/femsec/fiaa207] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/08/2020] [Indexed: 12/26/2022] Open
Abstract
Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.
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Affiliation(s)
- Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma/Unidad de Genómica Evolutiva, Departamento de Ecología y Evolución, Facultad de Ciencias/CURE, Universidad de la República, Maldonado, Uruguay
| | - Elena Beyhaut
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
| | - Andrew L Neal
- Department of Sustainable Agricultural Sciences, Rothamsted Research, North Wyke, Devon EX22 2SB, UK
| | - Nora Altier
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
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19
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Zhang X, Neal AL, Crawford JW, Bacq-Labreuil A, Akkari E, Rickard W. The effects of long-term fertilizations on soil hydraulic properties vary with scales. JOURNAL OF HYDROLOGY 2021; 593:125890. [PMID: 33612857 PMCID: PMC7871028 DOI: 10.1016/j.jhydrol.2020.125890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Soil structure is an indicator of soil quality and its alterations following cropping system conversion or fertilization change evolve slowly. How such alterations vary with scale remains elusive. We investigated this based on the Rothamsted long-term wheat experiment (since 1843) in the UK. Triplicate cores 7 cm high and 10 cm in diameter were taken from plots that have been under different fertilizations or returned to natural woodland for more than one century for imaging using X-ray computed tomography with the voxel size being 40 µm. We then broke each core and sampled three aggregates from it to scan with the voxel size being 1.5 µm. For each core and aggregate sample, we calculated its pore size distribution, permeability and tortuosity. The results showed that the fertilization change >170 years ago reshaped the soil structure differently between the core scale and the aggregate scale. Macro-porosity of the pores (>40 µm) in the cores unfertilized or fertilized with inorganic fertilizers was low and the pores were poorly connected in the top 10 cm of soil, compared to those given farmyard manure or in the woodland. In all treatments, the pores in the core images were hydraulically anisotropic with their permeability in the horizontal direction being higher than that in the vertical direction, whereas the aggregates were comparatively isotropic. The fertilization affected image porosity and permeability at core scale more significantly than at aggregate scale, and the aggregates fertilized with farmyard manure and in the woodland were more permeable than the aggregates in other treatments. It was also found that compared to no-fertilization or fertilization with complete fertilizers, fertilizing without phosphorus over the past 20 years increased the porosity and permeability of the aggregates but not of the cores. Fertilization with inorganic fertilizers increased the tortuosity of the macropores in the cores but not of the intra-aggregate pores, compared to no-fertilization. Porosity-permeability relationship for aggregates unfertilized or fertilized with inorganic fertilisers followed a power law with R 2 > 0.8. In contrast, the permeability of the aggregates in farmyard manure and in the woodland trended differently as their porosity increased. The results also revealed that the transport ability of the aggregates and cores responded differently to carbon in that with soil carbon increasing, the permeability of the aggregates increased asymptotically while the permeability of the cores, especially its horizontal component, increased exponentially.
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Affiliation(s)
- Xiaoxian Zhang
- Department of Sustainable Agricultural Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Andrew L Neal
- Sustainable Agriculture Sciences, Rothamsted Research, North Wyke EX20 2SB, UK
| | - John W Crawford
- Adam Smith Business School, University of Glasgow, West Quadrangle, Glasgow G12 8QQ. UK
| | - Aurelie Bacq-Labreuil
- Division of Agriculture & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Elsy Akkari
- Department of Sustainable Agricultural Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - William Rickard
- Department of Sustainable Agricultural Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
- Division of Agriculture & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
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20
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Harvey HJ, Wildman RD, Mooney SJ, Avery SV. Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments. Comput Struct Biotechnol J 2020; 18:2860-2866. [PMID: 33133427 PMCID: PMC7588748 DOI: 10.1016/j.csbj.2020.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022] Open
Abstract
Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.
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Affiliation(s)
- Harry J. Harvey
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ricky D. Wildman
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Corresponding author.
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