Comparing a simple arbuscular mycorrhizal fungal inoculum with commercial products for enhancing plant growth

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts forming mutualistic relationships with most land-plants. In AM symbiosis, the plant supplies the fungal partner with products of photosynthesis and in return recieves various mineral nutrients from the soil. Because of complex interactions with both soil and plants, disturbance can dramatically decrease AMF activity in soils and in these circumstances, it could be useful to restore AMF communities using inoculations. The use of AMF inoculants has so far been minimal due to the high cost and low availability of these products. In this study, the production of simple crude inocula was tested in trap cultures and the most suitable growth substrate nutrient content determined. The effectiveness of the produced inocula was compared with two commercially available inoculants. The results of this study indicate that the best substrate for inocula production in pot-cultures is pure sand with 5% natural soil. When using roots of plants grown in this manner as inoculants, the largest biomass and root-colonisation was achieved. As one of the commercial inoculants did not contain any mycorrhizal propagules at all, the need for quality control and establishment of industry standards is paramount. This study highlights the basics of using AM inoculations in home gardens and small-scale agriculture. The inoculation of large areas is still problematic because of low-yielding inoculant production, but could become highly perspective as methodology improves

Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety

Background and aim sSupporting arbuscular mycorrhizal (AM) nutrient acquisition in crops may reduce the need for fertilizer inputs, leading to more cost effective and sustainable crop production. In wheat, AM fungal responsiveness and benefits of symbiosis vary among varieties. This study explored the role of soil compaction in this variation.Methods We examined in a field experiment how soil compaction affects AM fungal colonization and biomass in five spring wheat varieties, and how these varieties differ in their AM-mediated phosphorus (P) uptake. We also studied soil properties, and AM fungal community composition in roots and soil.Results Soil compaction increased AM fungal colonization in the variety Alderon, characterized by root traits that indicate inefficient P uptake. Wheat P concentration and P:N ratio in Alderon and Diskett increased with increased root AM fungal colonization and biomass. In Diskett, which is the most cultivated spring wheat variety in Sweden and has intermediate root traits, total P content per m2 also increased with root AM fungal colonization and biomass.Conclusions Some wheat varieties, potentially those characterized by P inefficient root traits, such as Alderon, may depend more on AM-mediated P uptake in compacted than in non-compacted soil. Increased P uptake with increased AM fungal colonization in Diskett suggests that efficient root and AM-mediated nutrient uptake can occur simultaneously in a modern variety. Breeding varieties that use roots and AM symbiosis as complementary strategies for nutrient uptake could improve nutrient uptake efficiency and help farmers achieve stable yields in varying conditions

Metabarcoding of soil environmental DNA to estimate plant diversity globally

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Krohmseente tähtsus kestlikus põllumajanduses

Väitekirja elektrooniline versioon ei sisalda publikatsiooneDoktoritöö käigus uuriti taimede ja seente vahelist vastastikku kasulikku kooselu, mükoriisat, moodustavate mullaseente ökoloogiat põllumajandusmaastikes. Kuna nende seente abil saavad taimed mullast vajaminevaid toitaineid, on nad oluline osa mulla elustikust ning panustavad ka põllumajanduse jätkusuutlikkusse. Töö üks põhieesmärke oli uurida, kuidas levinud põlluharimise praktikad mükoriisaseeni mõjutavad ning millised praktikad võiksid nende elurikkust suurendada. Uuringutes leidsime, et sarnaselt Lääne-Euroopaga on ka Eestis olenevalt põlluharimise viisidest mükoriisaseente elurikkuses suured erinevused – mitmekesisemate ja vaesemate põldude mükoriisaseente liigirikkuse vahe oli koguni kuuekordne. Olulisteks negatiivseteks teguriteks olid sünteetiliste väetiste ja pestitsiidide kasutamine, kuid positiivselt mõjusid orgaaniliste väetiste kasutamine ja maastikuelementide rohkus. Lisaks saime teada, et lühiajaliste rohumaade lisamine külvikorda soodustab mullaseeni ning külvikorra planeerimisel tasuks mõelda kasvatatavate sortide valiku peale. Näiteks selgus, et mõned ajaloolised nisusordid kasvavad paremini koos mahetootmise põllu mullast pärit seentega, samas kui mõni kaasaegne sort jällegi intensiivtootmise mulla seentega. Selle teadmise baasilt oleks võimalik tulevikus aretada näiteks mükoriisasõbralikke sorte nii mahe- kui tavaviljelusse. Lisaks eksperimenteerisime ka liigirikaste taimekoosluste taastamisega, luues liigivaestesse põlevkivikarjääridesse mükoriisaseente abiga kõigest mõne aastaga rohelised niidud. Sama metoodikat kasutades võiks tekitada elurikkuse tugipunkte ka intensiivselt majandatud põllumajandusmaastikesse, kus taimede, putukate ja mükoriisaseente elustik põllumajandustootjale kasu saaks tuua. Seega, kasutades rohkem orgaanilisi väetisi ja tõrjudes haiguseid ning kahjureid mitmekesise külvikorraga saab luua mükoriisaseeni soodustavad tingimused. Lisades maastikesse veel uusi ja hoides olemasolevaid elurikkuse tugipunkte, võiksime olla eeskujuks oma kodukandi kõrge elurikkuse ja sellega arvestava toidutootmisega.This doctoral thesis provides a deeper understanding of the ecology of soil fungi that form mycorrhizas in arable landscapes. These fungi provide plants with much needed soil nutrients and are therefore a vital part of sustainable food production. One of the central aims was to understand how the common agricultural practices used in the fields affect these key fungi. In our studies we found that much like in the rest of Europe, there are large differences in the diversity of mycorrhizal fungi in arable field soils. Differences in mycorrhizal fungal richness between the most and least diverse fields were sixfold. The major factors decreasing mycorrhizal fungal diversity were the use of synthetic fertilizers and pesticides but also biodiversity impoverished agricultural landscapes. In addition, we learned that temporary grasslands within the crop rotations have important implications for sustaining soil fungal biodiversity. Furthermore, we found that the crop varieties sown can have an impact on mycorrhizal fungi, with some older varieties faring better in organically managed soils than newer breeds. Although the plants’ affinity to mycorrhizal fungi was not clearly dependant on the era a variety was bred, it does show that we should bear mycorrhizal associations in mind when breeding crops of the future. We also experimented with creating diverse vegetation assemblages in biodiversity impoverished landscapes, using depleted oil-shale quarries as a model system. We used native plants and sowed them onto the restoration sites together with the mycorrhizal fungi they naturally grow with. Using this methodology, we were able to bring dosens of plant species into a former biodiversity desert, highlighting the possibilities of restoring biodiversity hot-spots also in other areas. To conclude, we emphasize that safeguarding the biodiversity of vital mycorrhizal fungi is possible even with the measures available to farmers today. More organic fertilizers with diverse crop rotations for disease and weed control, accompanied by the biodiversity support of diverse landscapes is something that would pave the way for sustainable food production.https://www.ester.ee/record=b544943

Manipulating below ground diversity for above ground diversity: application of fungi for vegetation restoration

The loss and fragmentation of habitats is one of the main drivers of deteriorating ecosystem functioning and services. This has induced a growing need for conservation and increasingly more – restoration. A central part of land-ecosystems is soil biota with arbuscular mycorrhizal (AM) fungi being a key constituent. As ubiquitous plant symbionts, AM fungi have a global impact on carbon sequestration and nutrient cycling, soil formation, erosion and leaching processes, therefore influencing all spheres of earth. In soils where disturbance has lead to the loss of soil cover or a drastic change in plant community composition, the absence of suitable AM fungal symbionts can lead to slow post-restoration plant community recovery, with negative implications on ecosystem functioning for decades. Because of this, the manipulation of soil AM fungal composition for restoring plant communities is a highly promising perspective. To test the applicability of this idea, we have set up field inoculation experiments in three ecosystem restoration scenarios in Estonia: restoration of alvar grassland vegetation following clearing; restoration of wooded meadow vegetation following clearing; restoration of vegetation in depleted oil shale quarries. Native soils and plant seeds were collected from target ecosystems in good condition and trap cultures were set up to obtain bulk fungal inoculums. These inoculums were applied with native plant seeds in 18 restoration sites across Estonia. The experiment is monitored for effects and temporal changes in above and below-ground diversity, giving valuable insights into the practical implication of AM fungi for ecosystem restoration. An overview of the hypotheses, methodology and practical boundaries of this experiment will be given in tandem with results from year one of the experiment.peerReviewe

Different wheat cultivars exhibit variable responses to inoculation with arbuscular mycorrhizal fungi from organic and conventional farms.

The present study aimed to investigate the effects of arbuscular mycorrhizal (AM) fungal communities originating from organic and conventional agriculture on wheat growth and yield. Six different spring wheat cultivars released in different years in north and central European countries were considered. We hypothesised that AM fungal inoculum collected from organic agricultural fields would elicit a greater positive growth response than inoculum collected from conventional agricultural fields; and that older cultivars, which were developed under conditions of low fertilizer input, would exhibit overall greater growth responses to the presence of AM fungi, compared with more recent cultivars, and that AM fungal inoculum from conventional fields might have the most beneficial effect on the growth and yield of recent cultivars. The results showed that the overall effects on the growth and yield of spring wheat grown with organic and conventional AM fungal inocula did not differ greatly. However, the inoculation growth response, showing the difference of the effects of organic and conventional inocula, varied between particular wheat cultivars. Inoculation growth response of the cultivar Pikker (released in 1959) was the most positive, while that of the cultivar Arabella (released in 2012) was the most negative. The use of AM fungal inoculum from organic fields resulted in slightly taller plant individuals. Pikker showed relatively higher yield and stronger growth when the organic AM fungal inoculum was used. Arabella exhibited relatively lower yield and weaker growth when the organic inoculum was used. Whether the positive response of Pikker to Estonian organic inoculation reflects adaptation to the locally occurring AM fungal community needs to be established by further studies of the communities of AM fungi colonizing wheat roots

Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes

Grasslands are among the most threatened terrestrial biomes, and habitat conservation alone will be insufficient to meet biodiversity goals. While restoration of indigenous grasslands is a priority, conflict with economic objectives means that incorporation of alternative habitats is necessary to offset grassland loss. With up to 800,000 km2 of land affected by mining globally, there is an opportunity to create additional grassland habitat in post-mining landscapes. We aimed to assess whether co-introduction of native arbuscular mycorrhizal (AM) fungi and plants is an efficient means of initializing species-rich vegetation recovery in barren post-mining landscapes. We established an experiment in three post-mining areas in Estonia, where we seeded plots with native plant seeds and inoculated them with trap-cultured native AM fungi from a similar habitat. We measured the abundance and composition of soil AM fungal and above-ground plant communities in two consecutive years using relevés, high-throughput sequencing and fatty acid profiling. Our results demonstrate that co-introduction of native plants and AM fungi is an effective way to establish species-rich vegetation in post-mining areas. Co-introduction of symbiotic partners resulted in higher richness, diversity and abundance of plants and AM fungi than when either partner was introduced individually. However, the plant and AM fungal communities in sown and inoculated plots were not distinct from those in uninoculated treatments; they rather formed a subset of all taxa present on the sites but exhibited higher diversity than in uninoculated plots. Synthesis and applications. This study shows that managing the below-ground microbiome is an essential part of vegetation restoration. The availability of symbiotic partners can be considered a key aspect determining the diversity of restored vegetation. Targeted inoculations with native and habitat-specific native arbuscular mycorrhizal fungi could therefore increase restoration success