Toward Comprehensive Plant Microbiome Research

Microbes have driven eco-evolutionary adaptations organizing biodiversity from the origin of life. They are ubiquitous and abundant, facilitating the biochemical processes that make Earth habitable and shape ecosystem structures, functions, and services. Recent studies reveal that commensalistic and beneficial microbes associated with wild and domesticated plants may aid in establishing sustainable agriculture for a changing climate. However, developing microbe-based biotechnologies and ecosystem services requires a thorough understanding of the diversity and complexity of microbial interactions with each other and with higher organisms. We discuss the hot and blind spots in contemporary research on plant microbiomes, and how the latest molecular biological techniques and empirical eco-evolutionary approaches could elevate our perception of microbe-plant interactions through multidisciplinary studies

1,6-Dehydropinidine Is an Abundant Compound in Picea abies (Pinaceae) Sprouts and 1,6-Dehydropinidine Fraction Shows Antibacterial Activity against Streptococcus equi Subsp. equi

Knowledge about the defensive chemistry of coniferous trees has increased in recent years regarding a number of alkaloid compounds; in addition to phenolics and terpenes. Here, we show that Norway spruce (Picea abies (L.) H. Karst.), an important boreal zone tree species; accumulates 1,6-dehydropinidine (2-methyl-6-(2-propenyl)-1,6-piperideine) in its needles and bark. We reanalyzed previously published GC-MS data to obtain a full picture of 1,6-dehydropinidine in P. abies. 1,6-dehydropinidine appeared to especially accumulate in developing spring shoots. We used solid-phase partitioning to collect the alkaloid fraction of the sprouts and thin-layer chromatography to purify 1,6-dehydropinidine. The antibacterial properties of the 1,6-dehydropinidine fraction were tested using a broth microdilution method; with Streptococcus equi subsp. equi as a model organism. Based on our results 1,6-dehydropinidine is common in alkaloid extractions from P. abies (0.4 ± 0.03 mg g−1 dw in mature needles) and it is especially abundant in young spruce shoots (2.7 ± 0.5 mg g−1 dw). Moreover; 1,6-dehydropinidine extracted from P. abies sprouts showed mild antibacterial potential against Streptococcus equi subsp. equi (MIC 55 µg mL−1). The antibacterial activity of a plant compound thought of as an intermediate rather than an end-product of biosynthesis calls for more detailed studies regarding the biological function of these coniferous alkaloid

1,6-Dehydropinidine Is an Abundant Compound in Picea abies (Pinaceae) Sprouts and 1,6-Dehydropinidine Fraction Shows Antibacterial Activity against Streptococcus equi Subsp. equi

Knowledge about the defensive chemistry of coniferous trees has increased in recent years regarding a number of alkaloid compounds; in addition to phenolics and terpenes. Here, we show that Norway spruce (Picea abies (L.) H. Karst.), an important boreal zone tree species; accumulates 1,6-dehydropinidine (2-methyl-6-(2-propenyl)-1,6-piperideine) in its needles and bark. We reanalyzed previously published GC-MS data to obtain a full picture of 1,6-dehydropinidine in P. abies. 1,6-dehydropinidine appeared to especially accumulate in developing spring shoots. We used solid-phase partitioning to collect the alkaloid fraction of the sprouts and thin-layer chromatography to purify 1,6-dehydropinidine. The antibacterial properties of the 1,6-dehydropinidine fraction were tested using a broth microdilution method; with Streptococcus equi subsp. equi as a model organism. Based on our results 1,6-dehydropinidine is common in alkaloid extractions from P. abies (0.4 ± 0.03 mg g−1 dw in mature needles) and it is especially abundant in young spruce shoots (2.7 ± 0.5 mg g−1 dw). Moreover; 1,6-dehydropinidine extracted from P. abies sprouts showed mild antibacterial potential against Streptococcus equi subsp. equi (MIC 55 µg mL−1). The antibacterial activity of a plant compound thought of as an intermediate rather than an end-product of biosynthesis calls for more detailed studies regarding the biological function of these coniferous alkaloid

Plants assemble species specific bacterial communities from common core taxa in three arcto-alpine climate zones

Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high- arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.peerReviewe

Heritable Epichloe symbiosis shapes fungal but not bacterial communities of plant leaves

Keystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloe species of pooidae grasses modulate microbiota of their shared host plant

Valkoapilan ja typpilannoituksen vaikutus laitumen kivennäiskoostumukseen ja karitsoiden kivennäisten saantiin

Valkoapilan vaikutusta laiduntavan eläimen kivennäisten saantiin on tutkittu huomattavasti vähemmän kuin sen vaikutusta rehun sulavuuteen ja valkuaispitoisuuteen. Karitsoiden valkoapila- ja heinälaidun-koetta jatkettiin analysoimalla laidunten kivennäiskoostumus ja karitsoiden kivennäisten saanti kol-men vuoden tutkimusjakson aikana. Heinälaitumia oli kolme. Ne saivat typpeä 0, 120 tai 250 kg ha-1 vuodessa. Valkoapilaheinälaitumia oli yksi ja sitä ei lannoitettu typellä. Karitsat laidunsivat kaksi kolmesta viiteen viikon jaksoa kaikkien tutkimuskesien aikana.Valkoapilalaitumen valkoapilapitoisuus oli ensimmäisellä laidunjaksolla keskimäärin 25 % ja toisella 42 %. Laidunrehun kivennäispitoisuus (Ca, Mg, P, K, Se ja N) ja laidunrehun nitraattipitoisuus määritettiin. Syönnin määrittämiseen käytettiin n-alkaaneja merkkiaineena, minkä pohjalta laskettiin karitsoiden kivennäisten saanti. Laitumen typpilannoituksen tehokkuutta arvioitiin kriittisen typpikäyrän avulla.Valkoapilalaitumen laidunrehun kuiva-aineen kalsiumpitoisuus (7,8 vs 4,7 g kg-1), magnesiumpitoisuus (2,1 vs 1,8 g kg-1) ja Ca/P suhde (1,9 vs 1,2) olivat kaikki korkeampia kuin heinälaitumien. K/(Ca+Mg) -ekvivalenttisuhde (1,7 vs 2,5) oli matalampi valkoapilalaitumessa kuin heinälaitumessa. Karitsoiden kalsiuminsaanti oli riittävä valkoapilalaitumella, mutta jäi 50 %:iin tarpeesta heinälaitu-milla. Kasvilaji ei vaikuttanut fosfori-, kalium- ja seleenipitoisuuksiin. Kaikilla laitumilla fosforinsaanti oli riittävä, kaliuminsaanti liian suuri ja seleeninsaanti liian pieni tarpeeseen nähden. Typpilan-noitus lisäsi sekä kaliumin- (33,5 vs 38,5 g kg-1) että seleeninottoa (0,08 vs 0,14 mg kg-1) heinälaitumilla.Kriittisen typpikäyrän avulla tarkasteltuna pääosassa laitumia typen niukkuus rajoitti laitumen kuiva-aineen tuotantoa. Muutamalla korkeimman typpilannoituksen saaneella heinälaitumella todettiin sadonmuodostuksen kannalta turhan korkea kasvuston typpipitoisuus. Tämä tarkoittaa, että kaikki kasvissa oleva typpi ei tule käytetyksi kuiva-aineen ja valkuaisentuotantoon vaan kasviin alkaa kerääntyä nitraatteja. Näillä ruuduilla mitattiinkin karitsoille liian korkeita nitraattipitoisuuksia (>10 000 mg kg-1). Lisäksi karitsoilla ilmeni terveysongelmia samoilla ruuduilla. Seleeniä lukuun ottamatta valkoapilalaitumen kivennäiskoostumus oli karitsan kannalta heinälaidunta tasapainoisempi

Glyphosate residues alter the microbiota of a perennial weed with a minimal indirect impact on plant performance

Purpose In cold climates, glyphosate residues may linger in soils, with effects on plant-microbe interactions and, consequently, plant performance. Here, we explore the influence of glyphosate residues on the endophytic microbiota (bacteria and fungi) and performance of the perennial nitrogen-fixing weed Lupinus polyphyllus. Methods In a common garden, we grew plants from six populations of L. polyphyllus in glyphosate-treated or untreated control soils, with or without additional phosphorus. We sampled plant microbiota (leaves, roots, nodules) and assessed plant performance based on six traits: height, retrogression probability (i.e. shrinkage), biomass, root:shoot ratio, nodule number, and nodule viability. Results The richness of plant endophytic microbial communities was determined by soil phosphorus level rather than by glyphosate treatment. However, for bacteria, the composition of these communities differed between glyphosate-treated and control soils across plant tissue types; no difference was observed for fungi. The plant bacterial communities in both soil types were dominated by potential nitrogen-fixing bacteria belonging to family Bradyrhizobiaceae, and particularly so in glyphosate-treated soils. Overall, though, these changes in plant bacterial communities had a minor effect on plant performance: the only difference we detected was that the probability of retrogression was occasionally higher in glyphosate-treated soils than in control soils. Conclusion Our findings indicate that glyphosate-based herbicides, when applied at the recommended frequency and concentration, may not have critical effects on the growth of short-lived weeds after the safety period has passed; however, the endophytic microbiota of such weeds may experience longer-lasting shifts in community structure.</p