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Oddi L, Volpe V, Carotenuto G, Politi M, Barni E, Crosino A, Siniscalco C, Genre A. Boosting species evenness, productivity and weed control in a mixed meadow by promoting arbuscular mycorrhizas. FRONTIERS IN PLANT SCIENCE 2024; 15:1303750. [PMID: 38390295 PMCID: PMC10883063 DOI: 10.3389/fpls.2024.1303750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/08/2024] [Indexed: 02/24/2024]
Abstract
Lowland meadows represent aboveground and belowground biodiversity reservoirs in intensive agricultural areas, improving water retention and filtration, ensuring forage production, contrasting erosion and contributing to soil fertility and carbon sequestration. Besides such major ecosystem services, the presence of functionally different plant species improves forage quality, nutritional value and productivity, also limiting the establishment of weeds and alien species. Here, we tested the effectiveness of a commercial seed mixture in restoring a lowland mixed meadow in the presence or absence of inoculation with arbuscular mycorrhizal (AM) fungi and biostimulation of symbiosis development with the addition of short chain chito-oligosaccharides (CO). Plant community composition, phenology and productivity were regularly monitored alongside AM colonization in control, inoculated and CO-treated inoculated plots. Our analyses revealed that the CO treatment accelerated symbiosis development significantly increasing root colonization by AM fungi. Moreover, the combination of AM fungal inoculation and CO treatment improved plant species evenness and productivity with more balanced composition in forage species. Altogether, our study presented a successful and scalable strategy for the reintroduction of mixed meadows as valuable sources of forage biomass; demonstrated the positive impact of CO treatment on AM development in an agronomic context, extending previous observations developed under controlled laboratory conditions and leading the way to the application in sustainable agricultural practices.
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Affiliation(s)
- Ludovica Oddi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Veronica Volpe
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Gennaro Carotenuto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mara Politi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Elena Barni
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Crosino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Consolata Siniscalco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Naumova N, Barsukov P, Baturina O, Rusalimova O, Kabilov M. West-Siberian Chernozem: How Vegetation and Tillage Shape Its Bacteriobiome. Microorganisms 2023; 11:2431. [PMID: 37894089 PMCID: PMC10609427 DOI: 10.3390/microorganisms11102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs' richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0-5 cm of the undisturbed soil. As for the β-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production.
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Affiliation(s)
- Natalia Naumova
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Pavel Barsukov
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.B.); (M.K.)
| | - Olga Rusalimova
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.B.); (M.K.)
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Chertkova E, Kabilov MR, Yaroslavtseva O, Polenogova O, Kosman E, Sidorenko D, Alikina T, Noskov Y, Krivopalov A, Glupov VV, Kryukov VY. Links between Soil Bacteriobiomes and Fungistasis toward Fungi Infecting the Colorado Potato Beetle. Microorganisms 2023; 11:microorganisms11040943. [PMID: 37110366 PMCID: PMC10141481 DOI: 10.3390/microorganisms11040943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/02/2023] [Accepted: 04/02/2023] [Indexed: 04/07/2023] Open
Abstract
Entomopathogenic fungi can be inhibited by different soil microorganisms, but the effect of a soil microbiota on fungal growth, survival, and infectivity toward insects is insufficiently understood. We investigated the level of fungistasis toward Metarhizium robertsii and Beauveria bassiana in soils of conventional potato fields and kitchen potato gardens. Agar diffusion methods, 16S rDNA metabarcoding, bacterial DNA quantification, and assays of Leptinotarsa decemlineata survival in soils inoculated with fungal conidia were used. Soils of kitchen gardens showed stronger fungistasis toward M. robertsii and B. bassiana and at the same time the highest density of the fungi compared to soils of conventional fields. The fungistasis level depended on the quantity of bacterial DNA and relative abundance of Bacillus, Streptomyces, and some Proteobacteria, whose abundance levels were the highest in kitchen garden soils. Cultivable isolates of bacilli exhibited antagonism to both fungi in vitro. Assays involving inoculation of nonsterile soils with B. bassiana conidia showed trends toward elevated mortality of L. decemlineata in highly fungistatic soils compared to low-fungistasis ones. Introduction of antagonistic bacilli into sterile soil did not significantly change infectivity of B. bassiana toward the insect. The results support the idea that entomopathogenic fungi can infect insects within a hypogean habitat despite high abundance and diversity of soil antagonistic bacteria.
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Affiliation(s)
- Ekaterina Chertkova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Olga Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Elena Kosman
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Darya Sidorenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yury Noskov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Anton Krivopalov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Vadim Yu. Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
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Hermans SM, Lear G, Case BS, Buckley HL. The soil microbiome: An essential, but neglected, component of regenerative agroecosystems. iScience 2023; 26:106028. [PMID: 36844455 PMCID: PMC9947323 DOI: 10.1016/j.isci.2023.106028] [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: 02/04/2023] Open
Abstract
Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.
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Affiliation(s)
- Syrie M. Hermans
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Bradley S. Case
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Hannah L. Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
- Corresponding author
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Winnicki MH, Dunn RR, Winther-Jensen M, Jess T, Allin KH, Bruun HH. Does childhood exposure to biodiverse greenspace reduce the risk of developing asthma? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157853. [PMID: 35940273 DOI: 10.1016/j.scitotenv.2022.157853] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of inflammatory diseases is increasing in populations throughout the industrialized world. An increasing proportion of human populations grow up and live in urban areas, probably with reduced exposure to biodiversity, including diverse soil biotas. Decreased exposure to microorganisms from natural environments, in particular in early childhood, has been hypothesized to hamper development of the human immune system and lead to increasing risks of inflammatory diseases, such as asthma. We investigated 40,249 Danish individuals born 1995-2015. Percentage greenspace was assessed in a 2 km buffer around home addresses of individuals. The Danish Biodiversity Map, charting occurrence density of red-listed animals, plants and macrofungi, was used as a proxy for multi-taxon biodiversity. For asthma defined broadly, we found no evidence of decreasing risk of developing asthma with higher levels of biodiversity, while greenspace exposure was associated with higher risk of asthma. In contrast, exposure to total and biodiverse greenspace was associated with reduced risk of developing severe asthma. Exposure to farmland, which in Denmark is heavily industrialized cropland, also showed association with elevated risk of developing asthma, even at relatively low agricultural landcover. In the subset of children growing up in highly urbanized settings, we found high exposures to urban greenspace to be associated with reduced risk of developing asthma. Our results lend limited support to the hypothesis that childhood exposure to biodiverse environments reduces the risk of acquiring inflammatory diseases later in life. However, access to urban greenspace, such as parks, which typically harbour low levels of biodiversity, seems to reduce asthma risk, potentially through exposure to common soil microbiota. Our results suggest that effects of biodiversity exposure on human health is set by a balance between ecosystem services and disservices and that biodiversity conservation is best motivated with other arguments than reduction of risks from inflammatory diseases.
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Affiliation(s)
- Martin Holm Winnicki
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Matilde Winther-Jensen
- Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Kristine Højgaard Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Hans Henrik Bruun
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Soil Mycobiome Diversity under Different Tillage Practices in the South of West Siberia. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081169. [PMID: 36013348 PMCID: PMC9409700 DOI: 10.3390/life12081169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Managing soil biodiversity by reduced or no tillage is an increasingly popular approach. Soil mycobiome in Siberian agroecosystems has been scarcely studied; little is known about its changes due to tillage. We studied mycobiome in Chernozem under natural steppe vegetation and cropped for wheat by conventional or no tillage in a long-term field trial in West Siberia, Russia, by using ITS2 rDNA gene marker (Illumina MiSeq sequencing). Half of the identified OTUs were Ascomycota with 82% of the total number of sequence reads and showing, like other phyla (Basidiomycota, Zygomycota, Mortierellomycota, Chytridiomycota, Glomeromycota), field-related differential abundance. Several dominant genera (Mortierella, Chaetomium, Clonostachys, Gibberella, Fusarium, and Hypocrea) had increased abundance in both cropped soils as compared with the undisturbed one and therefore can be safely assumed to be associated with wheat residues. Fungal OTUs' richness in cropped soils was less than in the undisturbed one; however, no tillage shifted soil mycobiome composition closer to the latter, albeit, it was still similar to the ploughed soil, despite different organic matter and wheat residue content. The study provided the first inventory of soil mycobiome under different tillage treatments in the south of West Siberia, where wheat production is an important section of the regional economy.
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