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Peña-Ponton C, Diez-Rodriguez B, Perez-Bello P, Becker C, McIntyre LM, van der Putten WH, De Paoli E, Heer K, Opgenoorth L, Verhoeven KJF. High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5839-5856. [PMID: 38836523 PMCID: PMC11427840 DOI: 10.1093/jxb/erae262] [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: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/06/2024]
Abstract
DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
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Moore JC, Coleman DC, Dungy CT, Frank T, Galvin KA, de Ruiter PC, McKnight DM, Six J, van der Putten WH. Diana Wall: A Champion for lives underfoot. Proc Natl Acad Sci U S A 2024; 121:e2411980121. [PMID: 39133839 PMCID: PMC11348308 DOI: 10.1073/pnas.2411980121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024] Open
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Lustenhouwer N, Chaubet TMR, Melen MK, van der Putten WH, Parker IM. Plant-soil interactions during the native and exotic range expansion of an annual plant. J Evol Biol 2024; 37:653-664. [PMID: 38536056 DOI: 10.1093/jeb/voae040] [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: 08/05/2023] [Revised: 03/06/2024] [Accepted: 03/26/2024] [Indexed: 06/30/2024]
Abstract
Range expansions, whether they are biological invasions or climate change-mediated range shifts, may have profound ecological and evolutionary consequences for plant-soil interactions. Range-expanding plants encounter soil biota with which they have a limited coevolutionary history, especially when introduced to a new continent. Past studies have found mixed results on whether plants experience positive or negative soil feedback interactions in their novel range, and these effects often change over time. One important theoretical explanation is that plants locally adapt to the soil pathogens and mutualists in their novel range. We tested this hypothesis in Dittrichia graveolens, an annual plant that is both expanding its European native range, initially coinciding with climate warming, and rapidly invading California after human introduction. In parallel greenhouse experiments on both continents, we used plant genotypes and soils from 5 locations at the core and edge of each range to compare plant growth in soil inhabited by D. graveolens and nearby control microsites as a measure of plant-soil feedback. Plant-soil interactions were highly idiosyncratic across each range. On average, plant-soil feedbacks were more positive in the native range than in the exotic range. In line with the strongly heterogeneous pattern of soil responses along our biogeographic gradients, we found no evidence for evolutionary differentiation between plant genotypes from the core to the edge of either range. Our results suggest that the evolution of plant-soil interactions during range expansion may be more strongly driven by local evolutionary dynamics varying across the range than by large-scale biogeographic shifts.
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Cozim-Melges F, Ripoll-Bosch R, Veen GFC, Oggiano P, Bianchi FJJA, van der Putten WH, van Zanten HHE. Farming practices to enhance biodiversity across biomes: a systematic review. NPJ BIODIVERSITY 2024; 3:1. [PMID: 39242701 PMCID: PMC11332212 DOI: 10.1038/s44185-023-00034-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/20/2023] [Indexed: 09/09/2024]
Abstract
Intensive agriculture for food and feed production is a key driver of global biodiversity loss. It is generally assumed that more extensive practices are needed to reconcile food production with biodiversity conservation. In a literature review across biomes and for seven taxa, we retrieved 35 alternative practices (e.g. no-tillage, cover crops, organic fertilizer) from 331 studies. We found that no single practice enhanced all taxonomic groups, but that overall less intensive agricultural practices are beneficial to biodiversity. Nevertheless, often practices had no effects observed and very rarely contrasting impacts on aboveground versus belowground taxa. Species responses to practices were mostly consistent across biomes, except for fertilization. We conclude that alternative practices generally enhance biodiversity, but there is also variation in impacts depending on taxonomic group or type of practice. This suggests that a careful selection of practices is needed to secure biodiversity across taxa in future food systems worldwide.
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Bieluczyk W, Asselta FO, Navroski D, Gontijo JB, Venturini AM, Mendes LW, Simon CP, Camargo PBD, Tadini AM, Martin-Neto L, Bendassolli JA, Rodrigues RR, van der Putten WH, Tsai SM. Linking above and belowground carbon sequestration, soil organic matter properties, and soil health in Brazilian Atlantic Forest restoration. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118573. [PMID: 37459811 DOI: 10.1016/j.jenvman.2023.118573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 09/17/2023]
Abstract
Forest restoration mitigates climate change by removing CO2 and storing C in terrestrial ecosystems. However, incomplete information on C storage in restored tropical forests often fails to capture the ecosystem's holistic C dynamics. This study provides an integrated assessment of C storage in above to belowground subsystems, its consequences for greenhouse gas (GHG) fluxes, and the quantity, quality, and origin of soil organic matter (SOM) in restored Atlantic forests in Brazil. Relations between SOM properties and soil health indicators were also explored. We examined two restorations using tree planting ('active restoration'): an 8-year-old forest with green manure and native trees planted in two rounds, and a 15-year-old forest with native-planted trees in one round without green manure. Restorations were compared to reformed pasture and primary forest sites. We measured C storage in soil layers (0-10, 10-20, and 20-30 cm), litter, and plants. GHG emissions were assessed using CH4 and CO2 fluxes. SOM quantity was evaluated using C and N, quality using humification index (HLIFS), and origin using δ13C and δ15N. Nine soil health indicators were interrelated with SOM attributes. The primary forest presented the highest C stocks (107.7 Mg C ha-1), followed by 15- and 8-year-old restorations and pasture with 69.8, 55.5, and 41.8 Mg C ha-1, respectively. Soil C stocks from restorations and pasture were 20% lower than primary forest. However, 8- and 15-year-old restorations stored 12.3 and 28.3 Mg ha-1 more aboveground C than pasture. The younger forest had δ13C and δ15N values of 2.1 and 1.7‰, respectively, lower than the 15-year-old forest, indicating more C derived from C3 plants and biological N fixation. Both restorations and pasture had at least 34% higher HLIFS in deeper soil layers (10-30 cm) than primary forest, indicating a lack of labile SOM. Native and 15-year-old forests exhibited higher soil methane influx (141.1 and 61.9 μg m-2 h-1). Forests outperformed pasture in most soil health indicators, with 69% of their variance explained by SOM properties. However, SOM quantity and quality regeneration in both restorations approached the pristine forest state only in the top 10 cm layer, while deeper soil retained agricultural degradation legacies. In conclusion, active restoration of the Atlantic Forest is a superior approach compared to pasture reform for GHG mitigation. Nonetheless, the development of restoration techniques to facilitate labile C input into deeper soil layers (>10 cm) is needed to further improve soil multifunctionality and long-term C storage.
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Hesen V, Boele Y, Bakx-Schotman T, van Beersum F, Raaijmakers C, Scheres B, Willemsen V, van der Putten WH. Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:62. [PMID: 37468998 DOI: 10.1186/s40793-023-00511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome. RESULTS We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in. CONCLUSIONS Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
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Bieluczyk W, Merloti LF, Cherubin MR, Mendes LW, Bendassolli JA, Rodrigues RR, de Camargo PB, van der Putten WH, Tsai SM. Forest restoration rehabilitates soil multifunctionality in riparian zones of sugarcane production landscapes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 888:164175. [PMID: 37201828 DOI: 10.1016/j.scitotenv.2023.164175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Brazilian sugarcane plays a vital role in the production of both sugar and renewable energy. However, land use change and long-term conventional sugarcane cultivation have degraded entire watersheds, including a substantial loss of soil multifunctionality. In our study, riparian zones have been reforested to mitigate these impacts, protect aquatic ecosystems, and restore ecological corridors within the sugarcane production landscapes. We examined (i) how forest restoration enables rehabilitation of the soil's multifunctionality after long-term sugarcane cultivation and (ii) how long it takes to regain ecosystem functions comparable to those of a primary forest. We investigated a time series of riparian forests at 6, 15, and 30 years after starting restoration by planting trees (named 'active restoration') and determined soil C stocks, δ13C (indicative of C origin), as well as measures indicative of soil health. A primary forest and a long-term sugarcane field were used as references. Eleven soil physical, chemical, and biological indicators were used for a structured soil health assessment, calculating index scores based on soil functions. Forest-to-cane conversion reduced 30.6 Mg ha-1 of soil C stocks, causing soil compaction and loss of cation exchange capacity, thus degrading soil's physical, chemical, and biological functions. Forest restoration for 6-30 years recovered 16-20 Mg C ha-1 stored in soils. In all restored sites, soil functions such as supporting root growth, aerating the soil, nutrient storage capacity, and providing C energy for microbial activity were gradually recovered. Thirty years of active restoration was sufficient to reach the primary forest state in overall soil health index, multifunctional performance, and C sequestration. We conclude that active forest restoration in sugarcane-dominated landscapes is an effective way to restore soil multifunctionality approaching the level of the native forest in approximately three decades. Moreover, the C sequestration in the restored forest soils will help to mediate global warming.
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Li X, Zhao R, Li D, Wang G, Bei S, Ju X, An R, Li L, Kuyper TW, Christie P, Bender FS, Veen C, van der Heijden MGA, van der Putten WH, Zhang F, Butterbach-Bahl K, Zhang J. Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N 2O emissions from soil. MICROBIOME 2023; 11:45. [PMID: 36890606 PMCID: PMC9996866 DOI: 10.1186/s40168-023-01466-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/10/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N2O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N2O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N2O emissions of isolated N2O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments. RESULTS AMF hyphae reduced denitrification-derived N2O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N2O emissions in the hyphosphere was linked to N2O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N2O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene. CONCLUSIONS The cooperation between AMF and the N2O-reducing Pseudomonas residing on hyphae significantly reduce N2O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N2O consumption in nutrient-enriched microsites, and consequently reduce N2O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.
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van der Putten WH, Bardgett RD, Farfan M, Montanarella L, Six J, Wall DH. Soil biodiversity needs policy without borders. Science 2023; 379:32-34. [PMID: 36603087 DOI: 10.1126/science.abn7248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Soil health laws should account for global soil connections.
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Li K, Veen GF(C, ten Hooven FC, Harvey JA, van der Putten WH. Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities. Ecol Lett 2023; 26:37-52. [PMID: 36414536 PMCID: PMC10098829 DOI: 10.1111/ele.14129] [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: 04/11/2022] [Revised: 07/20/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil 'memories' that influence aboveground plant community interactions in the next growing season. These soil-borne 'memories' can be altered by climate warming-induced plant range shifts and extreme drought.
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Yang Q, Veen GF(C, Wagenaar R, Manrubia M, ten Hooven FC, van der Putten WH. Temporal dynamics of range expander and congeneric native plant responses during and after extreme drought events. ECOL MONOGR 2022; 92:e1529. [PMID: 36590329 PMCID: PMC9787952 DOI: 10.1002/ecm.1529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 01/14/2022] [Indexed: 01/04/2023]
Abstract
Climate change is causing range shifts of many species to higher latitudes and altitudes and increasing their exposure to extreme weather events. It has been shown that range-shifting plant species may perform differently in new soil than related natives; however, little is known about how extreme weather events affect range-expanding plants compared to related natives. In this study we used outdoor mesocosms to study how range-expanding plant species responded to extreme drought in live soil from a habitat in a new range with and without live soil from a habitat in the original range (Hungary). During summer drought, the shoot biomass of the range-expanding plant community declined. In spite of this, in the mixed community, range expanders produced more shoot biomass than congeneric natives. In mesocosms with a history of range expanders in the previous year, native plants produced less biomass. Plant legacy or soil origin effects did not change the response of natives or range expanders to summer drought. During rewetting, range expanders had less biomass than congeneric natives but higher drought resilience (survival) in soils from the new range where in the previous year native plant species had grown. The biomass patterns of the mixed plant communities were dominated by Centaurea spp.; however, not all plant species within the groups of natives and of range expanders showed the general pattern. Drought reduced the litter decomposition, microbial biomass, and abundances of bacterivorous, fungivorous, and carnivorous nematodes. Their abundances recovered during rewetting. There was less microbial and fungal biomass, and there were fewer fungivorous nematodes in soils from the original range where range expanders had grown in the previous year. We concluded that in mixed plant communities of range expanders and congeneric natives, range expanders performed better, under both ambient and drought conditions, than congeneric natives. However, when considering the responses of individual species, we observed variations among pairs of congenerics, so that under the present mixed-community conditions there was no uniformity in responses to drought of range expanders versus congeneric natives. Range-expanding plant species reduced soil fungal biomass and the numbers of soil fungivorous nematodes, suggesting that the effects of range-expanding plant species can trickle up in the soil food web.
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Li X, Zhang Z, Lü X, Li Y, Jin K, van der Putten WH. Soil aggregate microbiomes steer plant community overyielding in ungrazed and intensively grazed grassland soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115919. [PMID: 36001914 DOI: 10.1016/j.jenvman.2022.115919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Plant and soil microbial community composition play a central role in maintaining ecosystem functioning. Most studies have focused on soil microbes in the bulk soil, the rhizosphere and inside plant roots, however, less is known about the soil community that exists within soil aggregates, and how these soil communities influence plant biomass production. Here, using field-conditioned soil collected from experimental ungrazed and grazed grasslands in Inner Mongolia, China, we examined the composition of microbiomes inside soil aggregates of various size classes, and determined their roles in plant-soil feedbacks (PSFs), diversity-productivity relationships, and diversity-dependent overyielding. We found that grazing induced significantly positive PSF effects, which appeared to be mediated by mycorrhizal fungi, particularly under plant monocultures. Despite this, non-additive effects of microbiomes within different soil aggregates enhanced the strength of PSF under ungrazed grassland, but decreased PSF strength under intensively grazed grassland. Plant mixture-related increases in PSF effects markedly enhanced diversity-dependent overyielding, primarily due to complementary effects. Selection effects played far less of a role. Our work suggests that PSF contributes to diversity-dependent overyielding in grasslands via non-additive effects of microbiomes within different soil aggregates. The implication of our work is that assessing the effectiveness of sustainable grassland restoration and management on soil properties requires inspection of soil aggregate size-specific microbiomes, as these are relevant determinants of the feedback interactions between soil and plant performance.
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Thakur MP, Risch AC, van der Putten WH. Biotic responses to climate extremes in terrestrial ecosystems. iScience 2022; 25:104559. [PMID: 35784794 PMCID: PMC9240802 DOI: 10.1016/j.isci.2022.104559] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Anthropogenic climate change is increasing the incidence of climate extremes. Consequences of climate extremes on biodiversity can be highly detrimental, yet few studies also suggest beneficial effects of climate extremes on certain organisms. To obtain a general understanding of ecological responses to climate extremes, we present a review of how 16 major taxonomic/functional groups (including microorganisms, plants, invertebrates, and vertebrates) respond during extreme drought, precipitation, and temperature. Most taxonomic/functional groups respond negatively to extreme events, whereas groups such as mosses, legumes, trees, and vertebrate predators respond most negatively to climate extremes. We further highlight that ecological recovery after climate extremes is challenging to predict purely based on ecological responses during or immediately after climate extremes. By accounting for the characteristics of the recovering species, resource availability, and species interactions with neighboring competitors or facilitators, mutualists, and enemies, we outline a conceptual framework to better predict ecological recovery in terrestrial ecosystems.
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van Rijssel SQ, Veen GFC, Koorneef GJ, Bakx-Schotman JMTT, Ten Hooven FC, Geisen S, van der Putten WH. Soil microbial diversity and community composition during conversion from conventional to organic agriculture. Mol Ecol 2022; 31:4017-4030. [PMID: 35726521 PMCID: PMC9545909 DOI: 10.1111/mec.16571] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.
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Resch MC, Schütz M, Ochoa‐Hueso R, Buchmann N, Frey B, Graf U, van der Putten WH, Zimmermann S, Risch AC. Long‐term recovery of above‐and belowground interactions in restored grasslands after topsoil removal and seed addition. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Phillips HRP, Bach EM, Bartz MLC, Bennett JM, Beugnon R, Briones MJI, Brown GG, Ferlian O, Gongalsky KB, Guerra CA, König-Ries B, Krebs JJ, Orgiazzi A, Ramirez KS, Russell DJ, Schwarz B, Wall DH, Brose U, Decaëns T, Lavelle P, Loreau M, Mathieu J, Mulder C, van der Putten WH, Rillig MC, Thakur MP, de Vries FT, Wardle DA, Ammer C, Ammer S, Arai M, Ayuke FO, Baker GH, Baretta D, Barkusky D, Beauséjour R, Bedano JC, Birkhofer K, Blanchart E, Blossey B, Bolger T, Bradley RL, Brossard M, Burtis JC, Capowiez Y, Cavagnaro TR, Choi A, Clause J, Cluzeau D, Coors A, Crotty FV, Crumsey JM, Dávalos A, Cosín DJD, Dobson AM, Domínguez A, Duhour AE, van Eekeren N, Emmerling C, Falco LB, Fernández R, Fonte SJ, Fragoso C, Franco ALC, Fusilero A, Geraskina AP, Gholami S, González G, Gundale MJ, López MG, Hackenberger BK, Hackenberger DK, Hernández LM, Hirth JR, Hishi T, Holdsworth AR, Holmstrup M, Hopfensperger KN, Lwanga EH, Huhta V, Hurisso TT, Iannone BV, Iordache M, Irmler U, Ivask M, Jesús JB, Johnson-Maynard JL, Joschko M, Kaneko N, Kanianska R, Keith AM, Kernecker ML, Koné AW, Kooch Y, Kukkonen ST, Lalthanzara H, Lammel DR, Lebedev IM, Le Cadre E, Lincoln NK, López-Hernández D, Loss SR, Marichal R, Matula R, Minamiya Y, Moos JH, Moreno G, Morón-Ríos A, Motohiro H, Muys B, Neirynck J, Norgrove L, Novo M, Nuutinen V, Nuzzo V, Mujeeb Rahman P, Pansu J, Paudel S, Pérès G, Pérez-Camacho L, Ponge JF, Prietzel J, Rapoport IB, Rashid MI, Rebollo S, Rodríguez MÁ, Roth AM, Rousseau GX, Rozen A, Sayad E, van Schaik L, Scharenbroch B, Schirrmann M, Schmidt O, Schröder B, Seeber J, Shashkov MP, Singh J, Smith SM, Steinwandter M, Szlavecz K, Talavera JA, Trigo D, Tsukamoto J, Uribe-López S, de Valença AW, Virto I, Wackett AA, Warren MW, Webster ER, Wehr NH, Whalen JK, Wironen MB, Wolters V, Wu P, Zenkova IV, Zhang W, Cameron EK, Eisenhauer N. Global data on earthworm abundance, biomass, diversity and corresponding environmental properties. Sci Data 2021; 8:136. [PMID: 34021166 PMCID: PMC8140120 DOI: 10.1038/s41597-021-00912-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/01/2021] [Indexed: 12/30/2022] Open
Abstract
Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.
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Thakur MP, van der Putten WH, Wilschut RA, Veen GFC, Kardol P, van Ruijven J, Allan E, Roscher C, van Kleunen M, Bezemer TM. Plant-Soil Feedbacks and Temporal Dynamics of Plant Diversity-Productivity Relationships. Trends Ecol Evol 2021; 36:651-661. [PMID: 33888322 DOI: 10.1016/j.tree.2021.03.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Plant-soil feedback (PSF) and diversity-productivity relationships are important research fields to study drivers and consequences of changes in plant biodiversity. While studies suggest that positive plant diversity-productivity relationships can be explained by variation in PSF in diverse plant communities, key questions on their temporal relationships remain. Here, we discuss three processes that change PSF over time in diverse plant communities, and their effects on temporal dynamics of diversity-productivity relationships: spatial redistribution and changes in dominance of plant species; phenotypic shifts in plant traits; and dilution of soil pathogens and increase in soil mutualists. Disentangling these processes in plant diversity experiments will yield new insights into how plant diversity-productivity relationships change over time.
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Resch MC, Schütz M, Buchmann N, Frey B, Graf U, van der Putten WH, Zimmermann S, Risch AC. Evaluating long-term success in grassland restoration: an ecosystem multifunctionality approach. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02271. [PMID: 33615604 DOI: 10.1002/eap.2271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/04/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
It is generally assumed that restoring biodiversity will enhance diversity and ecosystem functioning. However, to date, it has rarely been evaluated whether and how restoration efforts manage to rebuild biodiversity and multiple ecosystem functions (ecosystem multifunctionality) simultaneously. Here, we quantified how three restoration methods of increasing intervention intensity (harvest only < topsoil removal < topsoil removal + propagule addition) affected grassland ecosystem multifunctionality 22 yr after the restoration event. We compared restored with intensively managed and targeted seminatural grasslands based on 13 biotic and abiotic, above- and belowground properties. We found that all three restoration methods improved ecosystem multifunctionality compared to intensively managed grasslands and developed toward the targeted seminatural grasslands. However, whereas higher levels of intervention intensity reached ecosystem multifunctionality of targeted seminatural grasslands after 22 yr, lower intervention missed this target. Moreover, we found that topsoil removal with and without seed addition accelerated the recovery of biotic and aboveground properties, and we found no negative long-term effects on abiotic or belowground properties despite removing the top layer of the soil. We also evaluated which ecosystem properties were the best indicators for restoration success in terms of accuracy and cost efficiency. Overall, we demonstrated that low-cost measures explained relatively more variation of ecosystem multifunctionality compared to high-cost measures. Plant species richness was the most accurate individual property in describing ecosystem multifunctionality, as it accounted for 54% of ecosystem multifunctionality at only 4% of the costs of our comprehensive multifunctionality approach. Plant species richness is the property that typically is used in restoration monitoring by conservation agencies. Vegetation structure, soil carbon storage and water-holding capacity together explained 70% of ecosystem multifunctionality at only twice the costs (8%) of plant species richness, which is, in our opinion, worth considering in future restoration monitoring projects. Hence, our findings provide a guideline for land managers how they could obtain an accurate estimate of aboveground-belowground ecosystem multifunctionality and restoration success in a highly cost-efficient way.
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Reinhart KO, Bauer JT, McCarthy‐Neumann S, MacDougall AS, Hierro JL, Chiuffo MC, Mangan SA, Heinze J, Bergmann J, Joshi J, Duncan RP, Diez JM, Kardol P, Rutten G, Fischer M, van der Putten WH, Bezemer TM, Klironomos J. Globally, plant-soil feedbacks are weak predictors of plant abundance. Ecol Evol 2021; 11:1756-1768. [PMID: 33614002 PMCID: PMC7882948 DOI: 10.1002/ece3.7167] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs estimated from controlled bioassays. We meta-analyzed results from 22 PSF experiments and found an overall positive correlation (0.12 ≤ r ¯ ≤ 0.32) between plant abundance in the field and PSFs across plant functional types (herbaceous and woody plants) but also variation by plant functional type. Thus, our analysis provides quantitative support that plant abundance has a general albeit weak positive relationship with PSFs across ecosystems. Overall, our results suggest that harmful soil biota tend to accumulate around and disproportionately impact species that are rare. However, data for the herbaceous species, which are most common in the literature, had no significant abundance-PSFs relationship. Therefore, we conclude that further work is needed within and across biomes, succession stages and plant types, both under controlled and field conditions, while separating PSF effects from other drivers (e.g., herbivory, competition, disturbance) of plant abundance to tease apart the role of soil biota in causing patterns of plant rarity versus commonness.
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Wandrag EM, Bates SE, Barrett LG, Catford JA, Thrall PH, van der Putten WH, Duncan RP. Phylogenetic signals and predictability in plant-soil feedbacks. THE NEW PHYTOLOGIST 2020; 228:1440-1449. [PMID: 32619298 PMCID: PMC7689780 DOI: 10.1111/nph.16768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/12/2020] [Indexed: 05/28/2023]
Abstract
There is strong evidence for a phylogenetic signal in the degree to which species share co-evolved biotic partners and in the outcomes of biotic interactions. This implies there should be a phylogenetic signal in the outcome of feedbacks between plants and the soil microbiota they cultivate. However, attempts to identify a phylogenetic signal in plant-soil feedbacks have produced mixed results. Here we clarify how phylogenetic signals could arise in plant-soil feedbacks and use a recent compilation of data from feedback experiments to identify: whether there is a phylogenetic signal in the outcome of plant-soil feedbacks; and whether any signal arises through directional or divergent changes in feedback outcomes with evolutionary time. We find strong evidence for a divergent phylogenetic signal in feedback outcomes. Distantly related plant species show more divergent responses to each other's soil microbiota compared with closely related plant species. The pattern of divergence implies occasional co-evolutionary shifts in how plants interact with soil microbiota, with strongly contrasting feedback responses among some plant lineages. Our results highlight that it is difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely related species tend to have more similar responses.
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Koorem K, Snoek BL, Bloem J, Geisen S, Kostenko O, Manrubia M, Ramirez KS, Weser C, Wilschut RA, van der Putten WH. Community-level interactions between plants and soil biota during range expansion. THE JOURNAL OF ECOLOGY 2020; 108:1860-1873. [PMID: 32999508 PMCID: PMC7508040 DOI: 10.1111/1365-2745.13409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level.Here we used a plant-soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. In these conditioned soils, we determined the composition of fungi and bacteria by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene respectively. Nematode community composition was determined by microscopy-based morphological identification. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives.We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most above-ground biomass in soils that were conditioned by plant communities distantly related to them. Synthesis. Communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant-soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.
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Geisen S, Wall DH, van der Putten WH. Challenges and Opportunities for Soil Biodiversity in the Anthropocene. Curr Biol 2020; 29:R1036-R1044. [PMID: 31593662 DOI: 10.1016/j.cub.2019.08.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biodiversity on Earth is strongly affected by human alterations to the environment. The majority of studies have considered aboveground biodiversity, yet little is known about whether biodiversity changes belowground follow the same patterns as those observed aboveground. It is now established that communities of soil biota have been substantially altered by direct human activities such as soil sealing, agricultural land-use intensification, and biological invasions resulting from the introduction of non-native species. In addition, altered abiotic conditions resulting from climate change have also impacted soil biodiversity. These changes in soil biodiversity can alter ecosystem functions performed by the soil biota, and therefore, human-induced global changes have a feedback effect on ecosystem services via altered soil biodiversity. Here, we highlight the major phenomena that threaten soil biodiversity, and we propose options to reverse the decline in soil biodiversity. We argue that it is essential to protect soil biodiversity as a rich reservoir that provides insurance against the changes wrought by the Anthropocene. Overall, we need to better understand the determinants of soil biodiversity and how they function, plan to avoid further losses, and restore soil biodiversity where possible. Safeguarding this rich biotic reservoir is essential for soil sustainability and, ultimately, the sustainability of human society.
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Schneijderberg M, Cheng X, Franken C, de Hollander M, van Velzen R, Schmitz L, Heinen R, Geurts R, van der Putten WH, Bezemer TM, Bisseling T. Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history. ISME JOURNAL 2020; 14:2433-2448. [PMID: 32641729 DOI: 10.1038/s41396-020-0695-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 12/26/2022]
Abstract
As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species' average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.
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van den Hoogen J, Geisen S, Wall DH, Wardle DA, Traunspurger W, de Goede RGM, Adams BJ, Ahmad W, Ferris H, Bardgett RD, Bonkowski M, Campos-Herrera R, Cares JE, Caruso T, de Brito Caixeta L, Chen X, Costa SR, Creamer R, da Cunha E Castro JM, Dam M, Djigal D, Escuer M, Griffiths BS, Gutiérrez C, Hohberg K, Kalinkina D, Kardol P, Kergunteuil A, Korthals G, Krashevska V, Kudrin AA, Li Q, Liang W, Magilton M, Marais M, Martín JAR, Matveeva E, Mayad EH, Mzough E, Mulder C, Mullin P, Neilson R, Nguyen TAD, Nielsen UN, Okada H, Rius JEP, Pan K, Peneva V, Pellissier L, da Silva JCP, Pitteloud C, Powers TO, Powers K, Quist CW, Rasmann S, Moreno SS, Scheu S, Setälä H, Sushchuk A, Tiunov AV, Trap J, Vestergård M, Villenave C, Waeyenberge L, Wilschut RA, Wright DG, Keith AM, Yang JI, Schmidt O, Bouharroud R, Ferji Z, van der Putten WH, Routh D, Crowther TW. A global database of soil nematode abundance and functional group composition. Sci Data 2020; 7:103. [PMID: 32218461 PMCID: PMC7099023 DOI: 10.1038/s41597-020-0437-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 11/14/2022] Open
Abstract
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
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Lubbers IM, Berg MP, De Deyn GB, van der Putten WH, van Groenigen JW. Soil fauna diversity increases CO 2 but suppresses N 2 O emissions from soil. GLOBAL CHANGE BIOLOGY 2020; 26:1886-1898. [PMID: 31587448 PMCID: PMC7078878 DOI: 10.1111/gcb.14860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Soil faunal activity can be a major control of greenhouse gas (GHG) emissions from soil. Effects of single faunal species, genera or families have been investigated, but it is unknown how soil fauna diversity may influence emissions of both carbon dioxide (CO2 , end product of decomposition of organic matter) and nitrous oxide (N2 O, an intermediate product of N transformation processes, in particular denitrification). Here, we studied how CO2 and N2 O emissions are affected by species and species mixtures of up to eight species of detritivorous/fungivorous soil fauna from four different taxonomic groups (earthworms, potworms, mites, springtails) using a microcosm set-up. We found that higher species richness and increased functional dissimilarity of species mixtures led to increased faunal-induced CO2 emission (up to 10%), but decreased N2 O emission (up to 62%). Large ecosystem engineers such as earthworms were key drivers of both CO2 and N2 O emissions. Interestingly, increased biodiversity of other soil fauna in the presence of earthworms decreased faunal-induced N2 O emission despite enhanced C cycling. We conclude that higher soil fauna functional diversity enhanced the intensity of belowground processes, leading to more complete litter decomposition and increased CO2 emission, but concurrently also resulting in more complete denitrification and reduced N2 O emission. Our results suggest that increased soil fauna species diversity has the potential to mitigate emissions of N2 O from soil ecosystems. Given the loss of soil biodiversity in managed soils, our findings call for adoption of management practices that enhance soil biodiversity and stimulate a functionally diverse faunal community to reduce N2 O emissions from managed soils.
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