scholarly journals Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12236
Author(s):  
Lukas Beule ◽  
Petr Karlovsky
Keyword(s):  
Community Composition ◽  
Fungal Biomass ◽  
Soil Fungi ◽  
Alley Cropping ◽  
Arable Land ◽  
Agroforestry Systems ◽  
West Germany ◽  
Fungal Communities ◽  
Temperate Agroforestry ◽  
Fungal Populations

Background Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood. Methods Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing. Results Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi. Conclusions The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

scholarly journals Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246919
Author(s):  
Lukas Beule ◽  
Petr Karlovsky
Keyword(s):  
Bacterial Communities ◽  
Alley Cropping ◽  
Arable Land ◽  
Soil Microbial Communities ◽  
Agroforestry Systems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Bacterial Communities ◽  
Temperate Agroforestry ◽  
Soil Bacterial

Background Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce. Methods Here, we assessed the effect of temperate agroforestry on the abundance, diversity and composition of soil bacterial communities at three paired poplar-based alley cropping and conventional monoculture cropland systems using real-time PCR and Illumina sequencing of bacterial 16S rRNA genes. Two of the three systems grew summer barley (Hordeum vulgare); one system grew maize (Zea mays) in the sampling year. To capture the spatial heterogeneity induced by the tree rows, soil samples in the agroforestry systems were collected along transects spanning from the centre of the tree rows to the centre of the agroforestry crop rows. Results Tree rows of temperate agroforestry systems increased the abundance of soil bacteria while their alpha diversity remained largely unaffected. The composition of the bacterial communities in tree rows differed from those in arable land (crop rows of the agroforestry systems and conventional monoculture croplands). Several bacterial groups in soil showed strong association with either tree rows or arable land, revealing that the introduction of trees into arable land through agroforestry is accompanied by the introduction of a tree row-associated microbiome. Conclusion The presence of tree row-associated bacteria in agroforestry increases the overall microbial diversity of the system. We speculate that the increase in biodiversity is accompanied by functional diversification. Differences in plant-derived nutrients (root exudates and tree litter) and management practices (fertilization and tillage) likely account for the differences between bacterial communities of tree rows and arable land in agroforestry systems.

The effect of long-term nutrient deficiency on the abundance and community composition of arbuscular mycorrhizal fungi in a mountainous grassland

2021 ◽  
Author(s):  
Kian Jenab ◽  
Stefan Gorka ◽  
Sean Darcy ◽  
Lucia Fuchslueger ◽  
Alberto Canarini ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Community Composition ◽  
Plant Community ◽  
Fungal Biomass ◽  
Nutrient Deficiency ◽  
Soil Nutrient ◽  
Am Fungi ◽  
Fungal Communities ◽  
Plant Community Composition

<p>Arbuscular mycorrhiza (AM) fungi are associated with almost all land plants and provide soil nutrients and other benefits to their plant hosts in exchange for photosynthetic products. While fertilization regimes in managed grasslands or agricultural systems are tailored for increasing plant biomass, their potential effects on AM fungi are rarely taken into account. Nutrient-driven changes in abundance and community composition of AM fungi, however, may feedback on ecosystem performance in the long term. Therefore, it is necessary to get a better understanding on how AM fungal communities respond to changes and imbalances in soil nutrient availabilities.</p><p>Here, we evaluated how long-term nutrient deficiency of phosphorus (P), nitrogen (N) and potassium (K) affects the abundance and community composition of AM fungi in a mountainous grassland. In addition, we investigated how the responses of AM fungi to those deficiencies were modulated by liming and the type of fertilizer addition (inorganic versus organic).</p><p>Our study was carried out on a long-term nutrient deficiency experimental grassland site in Admont (Styria, Austria), established in 1946. Different fertilization treatments were applied for more than 70 years in a randomized block design, including numerous combinations of inorganic (P, N, K with/without lime) and organic (solid manure and liquid slurry) fertilizers. The hay meadow at the site is cut three times per year and biomass is not returned to the system. Therefore, biomass and nutrients have been continuously removed for decades, leading to different types of soil nutrient deficiency. In this study, we collected both root and soil samples in July 2019 and quantified AM fungi and other microbial groups by measuring neutral fatty acid (NLFA) and phospholipid fatty acid (PLFA) biomarkers, respectively. Additionally, we applied DNA and RNA-based amplicon sequencing of the 18S rRNA gene to identify AM fungal community composition.</p><p>Our data shows that deficiencies of one or more elements had a major impact on both AM fungal biomass and community composition. AM fungal biomass was higher in plots that received no fertilizers compared to inorganically fertilized plots, but lower in plots which were deficient only in certain single or multiple elements, specifically in plots fertilized with inorganic N only (i.e., deficient in P and K). Conversely, liming and organic fertilizer amendments increased AM fungal biomass compared to plots containing inorganic fertilizers without lime. Across all treatments, AM fungal biomass was positively correlated with pH and soil water content, and negatively with dissolved N compounds, indicating indirect effects via responses of other soil parameters to nutrient deficiency. Long-term nutrient deficiency also altered plant community composition, which may also have indirectly affected AM fungal communities.</p><p>We conclude that long-term nutrient deficiency, and in particular the stoichiometry of available nutrients, strongly affects the abundance and community composition of AM fungi in grassland soil. This response may be linked to changes in plant community composition or soil chemistry both as a result and as a cause, emphasizing the complexity of feedbacks determining the response of grassland ecosystems to changing nutrient conditions.</p>

scholarly journals Biomass Performance and Competition Effects in an Established Temperate Agroforestry System of Willow and Grassland—Results of the 2nd Rotation

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1819
Author(s):  
Rüdiger Graß ◽  
Sarah Malec ◽  
Michael Wachendorf
Keyword(s):  
Alley Cropping ◽  
Total Yield ◽  
Cropping System ◽  
Agroforestry Systems ◽  
Climatic Conditions ◽  
Pure Stand ◽  
Agricultural Practice ◽  
Temperate Agroforestry ◽  
Competition Effects ◽  
Border Areas

Agroforestry systems (AFSs) are promoted as environmentally friendly and climate-change-resilient cultivation systems with the potential of increasing ecosystem services. Especially under temperate climatic conditions, the implementation in agricultural practice is low so far, inter alia due to the lack of knowledge regarding longer-term effects of such systems. This study investigated biomass yields and crop development during the second rotation of an alley cropping system with willows (clone “Tordis” ((Salix schwerinii x S. viminalis) x S. vim.)) and grassland that was established in March 2011, as reported in a former study of the authors. Two grassland swards (white clover grass (Lolium perenne L. and Trifolium repens L.) (CG) and a diversity mixture with 32 plant species (DIV)) were proven in an intensive (3/4 cuts per year) and extensive management system (two cuts per year). Total yield (sum of three years) of AFS increased substantially in the second rotation (year four to six after establishment of the AFS). This was particularly due to a fivefold increase in woody biomass. At the same time, yields of grassland biomass decreased slightly. Biomass of CG outperformed DIV, especially in the intensive managed systems with a dry matter (DM) yield of 18 t ha−1, compared to 12.6 t ha−1. However, AFS grassland yields were always lower than yields of reference areas with grassland in pure stand. Nevertheless, lower yields are probably caused by competition effects between woody crops and grassland. Grassland yields along transects across the grassland alleyways showed a strong decrease in the border areas in all treatments. Higher grassland yields in the alley center did not compensate yield reductions in border areas. Furthermore, the botanical composition of grassland was modified in border areas with reduced legume DM contribution and increases of both grasses and forbs. Thus, the width of grassland alleys with 9 m caused strong competition effects by the willows.

scholarly journals Response of Soil Fungal Diversity and Community Composition to Varying Levels of Bamboo Biochar in Red Soils

2021 ◽  
Vol 9 (7) ◽  
pp. 1385
Author(s):  
Muhammad Waqqas Khan Tarin ◽  
Lili Fan ◽  
Dejin Xie ◽  
Muhammad Tayyab ◽  
Jundong Rong ◽  
...  
Keyword(s):  
Community Composition ◽  
Soil Ph ◽  
Soil Fungi ◽  
Nutrient Dynamics ◽  
Red Soil ◽  
Influential Factor ◽  
Stress Factors ◽  
Fungal Communities ◽  
Acidic Soils ◽  
The Impact

Soil fungi play a vital role in soil nutrient dynamics, but knowledge of their diversity and community composition in response to biochar addition into red soil is either limited or inconsistent. Therefore, we determined the impact of bamboo biochar (BB) with increasing concentrations (0, 5, 20, and 80 g kg−1 of soil, referred to as B0, BB5, BB20, and BB80, respectively) on soil physicochemical properties and fungal communities (Illumina high-throughput sequencing) in red soil under Fokenia hodginsii (Fujian cypress). We found that increasing BB levels effectively raised the soil pH and soil nutrients, particularly under BB80. BB addition significantly increased the relative abundance of important genera, i.e., Basidiomycota, Mucoromycota, and Chytridiomycota that could play a key role in ecological functioning, e.g., wood degradation and litter decomposition, improvement in plant nutrients uptake, and resistance to several abiotic stress factors. Soil amended with BB exhibited a substantial ability to increase the fungal richness and diversity; BB80 > BB20 > BB5 > B0. Basidiomycota, Mucoromycota, Glomeromycota, Rozellomycota, Aphelidiomycota, Kickxellomycota, and Planctomycetes were positively associated with soil pH, total nitrogen, phosphorous, and carbon, and available potassium and phosphorous. Besides, the correlation analysis between the soil fungal communities and soil properties also showed that soil pH was the most influential factor in shaping the soil fungal communities in the red soil. These findings have significant implications for a comprehensive understanding of how to ameliorate acidic soils with BB addition, as well as for future research on sustainable forest management, which might increase soil fungi richness, diversity, and functionality in acidic soils.

scholarly journals Relative Abundances of Species or Sequence Variants Can Be Misleading: Soil Fungal Communities as an Example

2021 ◽  
Vol 9 (3) ◽  
pp. 589
Author(s):  
Lukas Beule ◽  
Markus Arndt ◽  
Petr Karlovsky
Keyword(s):  
Population Size ◽  
Soil Fungi ◽  
Alley Cropping ◽  
Amplicon Sequencing ◽  
Environmental Benefits ◽  
Plant Production ◽  
Sequence Variants ◽  
Sequencing Analysis ◽  
Temperate Agroforestry ◽  
Relative Abundances

Plant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in temperate agroforestry systems are scarce, leaving our understanding of agricultural systems under agroforestry practice incomplete. Here, we assessed the composition and diversity of the soil fungal community as well as the frequency (relative abundance) of fungal groups in three paired temperate poplar-based alley cropping (agroforestry) and monoculture cropland systems by amplicon sequencing. Analysis of microbiomes using relative abundances of species or sequence variants obtained from amplicon sequencing ignores microbial population size, which results in several problems. For example, species stimulated by environmental parameters may appear unaffected or suppressed in amplicon counts. Therefore, we determined absolute abundances of selected fungal groups as well as total fungal population size by real-time polymerase chain reaction (PCR). Tree rows strongly affected the community composition and increased the population size and species richness of soil fungi. Furthermore, ectomycorrhiza were strongly promoted by the tree rows. We speculate that mycorrhiza improved the nutrient acquisition in unfertilized tree rows, thereby contributing to the total productivity of the system. Comparison of relative and absolute abundances revealed dramatic discrepancies, highlighting that amplicon sequencing alone cannot adequately assess population size and dynamics. The results of our study highlight the necessity of combining frequency data based on amplicon sequencing with absolute quantification.

scholarly journals Root Exudates Regulate Soil Fungal Community Composition and Diversity

2007 ◽  
Vol 74 (3) ◽  
pp. 738-744 ◽  
Author(s):  
Corey D. Broeckling ◽  
Amanda K. Broz ◽  
Joy Bergelson ◽  
Daniel K. Manter ◽  
Jorge M. Vivanco
Keyword(s):  
Community Composition ◽  
Root Exudates ◽  
Fungal Community ◽  
Fungal Biomass ◽  
Critical Role ◽  
Fungal Community Composition ◽  
General Role ◽  
Soil Fungal Community ◽  
Fungal Populations ◽  
Soil Fungal Community Composition

ABSTRACT Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species (Arabidopsis thaliana and Medicago truncatula) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.

scholarly journals Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations

2020 ◽  
Vol 8 (10) ◽  
pp. 1577
Author(s):  
Johannes Ballauff ◽  
Delphine Clara Zemp ◽  
Dominik Schneider ◽  
Bambang Irawan ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
Community Composition ◽  
Oil Palm ◽  
Soil Fungi ◽  
Structural Complexity ◽  
Tree Diversity ◽  
Ecological Crisis ◽  
Fungal Communities ◽  
Soil Microbiome ◽  
Abiotic Conditions ◽  
The Impact

Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

scholarly journals Effects of rhizosphere fungi on the chemical composition of fruits of the medicinal plant Cinnamomum migao endemic to southwestern China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingzhong Chen ◽  
Xiaolong Huang ◽  
Bingli Tong ◽  
Deng Wang ◽  
Jiming Liu ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Fungal Community ◽  
Small Population ◽  
Biologically Active ◽  
Fungal Communities ◽  
Chemical Components ◽  
Rhizosphere Fungi ◽  
Medicinal Value ◽  
Main Driver ◽  
Fungal Populations

Abstract Background This study examined how rhizosphere fungi influence the accumulation of chemical components in fruits of a small population species of Cinnamomum migao. Results Ascomycota and Basidiomycota were dominant in the rhizosphere fungal community of C. migao. Pestalotiopsis and Gibellulopsis were associated with α-Terpineol and sabinene content, and Gibellulopsis was associated with crude fat and carbohydrate content. There were significant differences in rhizosphere fungal populations between watersheds, and there was no obvious change between fruiting periods. Gibberella, Ilyonectria, Micropsalliota, and Geminibasidium promoted sabinene accumulation, and Clitocybula promoted α-Terpineol accumulation. Conclusion The climate-related differentiation of rhizosphere fungal communities in watershed areas is the main driver of the chemical composition of C. migao fruit. The control of the production of biologically active compounds by the rhizosphere fungal community provides new opportunities to increase the industrial and medicinal value of the fruit of C. migao.

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