Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

In both managed and natural ecosystems, beneficial plant-associated bacteria play a key role in supporting and/or increasing plant health and growth. Plant growth-promoting bacteria (PGPB) can be applied in agricultural production or for the phytoremediation of pollutants. However, because of their capacity to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. The majority of plant-associated bacteria derives from the soil environment. They may migrate to the rhizosphere and subsequently the rhizoplane of their hosts before they are able to show beneficial effects. Some rhizoplane colonizing bacteria can also penetrate plant roots, and some strains may move to aerial plant parts, with a decreasing bacterial density in comparison to rhizosphere or root colonizing populations. A better understanding on colonization processes has been obtained mostly by microscopic visualisation as well as by analysing the characteristics of mutants carrying disfunctional genes potentially involved in colonization. In this review we describe the individual steps of plant colonization and survey the known mechanisms responsible for rhizosphere and endophytic competence. The understanding of colonization processes is important to better predict how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilisers or biocontrol agents.     

Fungal growth on a common wood substrate across a tropical elevation gradient: Temperature sensitivity, community composition, and potential for above-ground decomposition

Fungal breakdown of plant material rich in lignin and cellulose (i.e. lignocellulose) is of central importance to terrestrial carbon (C) cycling due to the abundance of lignocellulose above and below-ground. Fungal growth on lignocellulose is particularly influential in tropical forests, as woody debris and plant litter contain between 50% and 75% lignocellulose by weight, and can account for 20% of the C stored in these ecosystems. In this study, we evaluated factors affecting fungal growth on a common wood substrate along a wet tropical elevation gradient in the Peruvian Andes. We had three objectives: 1) to determine the temperature sensitivity of fungal growth - i.e. Q₁₀, the factor by which fungal biomass increases given a 10 °C temperature increase; 2) to assess the potential for above-ground fungal colonization and growth on lignocellulose in a wet tropical forest; and 3) to characterize the community composition of fungal wood decomposers across the elevation gradient. We found that fungal growth had a Q₁₀ of 3.93 (95% CI of 2.76-5.61), indicating that fungal biomass accumulation on the wood substrate nearly quadrupled with a 10 °C increase in temperature. The Q₁₀ for fungal growth on wood at our site is higher than Q₁₀ values reported for litter decomposition in other tropical forests. Moreover, we found that above-ground fungal growth on the wood substrate ranged between 37% and 50% of that measured in the soil, suggesting above-ground breakdown of lignocellulose represents an unexplored component of the C cycle in wet tropical forests. Fungal community composition also changed significantly along the elevation gradient, and Ascomycota were the dominant wood decomposers at all elevations. Fungal richness did not change significantly with elevation, directly contrasting with diversity patterns observed for plant and animal taxa across this gradient. Significant variation in fungal community composition across the gradient suggests that the characteristics of fungal decomposer communities are, directly or indirectly, influenced by temperature.     

Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil

Soil pH is one of the most influential variables in soil, and is a powerful factor in influencing the size, activity and community structure of the soil microbial community. It was previously shown in a century old artificial pH gradient in an arable soil (pH 4.0-8.3) that bacterial growth is positively related to pH, while fungal growth increases with decreasing pH. In an attempt to elucidate some of the mechanisms for this, plant material that especially promotes fungal growth (straw) or bacterial growth (alfalfa) was added to soil samples of the pH gradient in 5-day laboratory incubation experiments. Also, bacterial growth was specifically inhibited by applying a selective bacterial growth inhibitor (bronopol) along the entire pH gradient to investigate if competitive interaction caused the shift in the decomposer community along the gradient. Straw benefited fungal growth relatively more than bacterial, and vice versa for alfalfa. The general pattern of a shift in fungal:bacterial growth with pH was, however, unaffected by substrate additions, indicating that lack of a suitable substrate was not the cause of the pH effect on the microbial community. In response to the bacterial growth inhibition by bronopol, there was stimulation of fungal growth up to pH 7, but not beyond, both for alfalfa and straw addition. However, the accumulation of ergosterol (an indicator of fungal biomass) during the incubation period after adding alfalfa increased at all pHs, indicating that fungal growth had been high at some time during the 5-day incubation following joint addition of alfalfa and bronopol. This was corroborated in a time-series experiment. In conclusion, the low fungal growth at high pH in an arable soil was caused to a large extent by bacterial competition, and not substrate limitation.     

Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9

The phospholipid fatty acid biomarkers 18:1ω9, 18:2ω6,9 and 18:3ω3,6,9 are commonly used as fungal biomarkers in soils. They have, however, also been found to occur in plant tissues, such as roots. Thus, the use of these PLFAs as fungal biomarkers in sieved soil, which may still contain small remains of roots, has been questioned. We used data from a recent beech tree girdling experiment to calculate the contribution of roots to these biomarkers and were able to demonstrate that not more than 0.61% of 18:1ω9 and 18:2ω6,9 in sieved soil samples originated from roots (but 4% of 18:3ω3,6,9). Additionally, the abundance of the biomarker 18:2ω6,9 in the soil was found to be highly correlated to ectomycorrhizal root colonization, which further corroborates its fungal origin. PLFA biomarkers were substantially reduced in vital roots from girdled trees compared to roots of control trees (by up to 76%), indicating that the major part of PLFAs measured in roots may actually originate from ectomycorrhizal fungi growing inside the roots. We calculated, that even a near to 50% reduction in fine root biomass - as observed in the girdling treatment - accounted for only 0.8% of the measured decrease of 18:2ω6,9. Our results demonstrate that both 18:1ω9 and 18:2ω6,9 are suitable biomarkers for detecting fungal dynamics in soils and that especially 18:2ω6,9 is a reliable biomarker to study mycorrhizal dynamics in beech forests.     

Identification of sources of resistance to damping-off and early root/hypocotyl damage from Rhizoctonia solani in common bean (Phaseolus vulgaris L.)

Rhizoctonia solani causes economically important root and hypocotyl diseases in common bean throughout the world. Root health is a vital factor in plant development and root diseases would negatively influence water and nutrient uptake as well as cause direct stand reduction and root rot damage to the crop. An efficient common bean screening method to evaluate damping-off and early root/hypocotyl damage from R. solani was developed and used to identify dry bean lines with levels of resistance to this disease. Two sets of 163 and 111 lines previously evaluated for drought tolerance in Nebraska and Puerto Rico were evaluated for damping-off resistance and early root/hypocotyl damage under greenhouse conditions. Disease severity on plants was identified based on above-ground symptoms, seedling survival and root lesions using a rating scale of 1 (resistant) to 9 (susceptible). In the first set of lines representing commonly grown dry bean cultivars, germplasm and sources of damping-off resistance, the Rhizoctonia mean rating ranged from 1.7 to 3.9; Phaseolus vulgaris lines PI 310668 and PI 533249 had the highest damping-off resistance. In the second set of the best lines from a drought tolerance shuttle breeding program the Rhizoctonia mean rating was between 2.6 and 5.7. The availability of drought tolerant dry bean lines allowed the testing of the hypothesis that there was a correlation between selecting for drought tolerance and R. solani damping-off resistance. No correlation between mean disease rating and drought tolerance was found, but adapted dry bean lines such as NE14-08-176 released as SB-DT1, and NE14-08-225 were identified with moderate damping-off resistance and drought tolerance. Lines with both traits and other attributes will facilitate development of resistant bean cultivars to manage damping-off caused by R. solani.     

长期不同氮肥施用量对潮土团聚体分布和真菌群落组成的影响

不同氮肥施用量显著改变团聚体分布、真菌群落组成及生物胶结物质的产生，但它们之间是否存在相关性尚不清楚。以中国科学院封丘农业生态实验站长期定位试验（2005—2020年）为研究平台，其包含5个施氮水平：0（F0）、150 kg?hm-2（F1）、190 kg?hm-2（F2）、230 kg?hm-2（F3）和270 kg?hm-2（F4），研究了不同施氮量对土壤团聚体组成（>2 000 μm、2 000～250 μm、250～53 μm和<53 μm）的影响，以及团聚体组成与生物胶结物质（球囊霉素相关土壤蛋白（GRSP）及微生物生物量碳（MBC））和土壤真菌之间的相关关系。结果表明，土壤团聚体分布和真菌群落组成分为显著不同的3组，分别为F0、F1和F2以及F3和F4，其中，（1）F1和F2处理团聚体平均重量直径（MWD）最高，同时大于2 000 μm团聚体的质量比例显著增加，并与拟棘壳孢属（Pyrenochaetopsis）富集有关；（2）F1和F2、F3和F4处理均表现为2 000～250 μm团聚体的质量比例增加，而小于53 μm粉黏粒质量比例显著降低，2 000～250 μm团聚体的质量比例增加主要与易提取球囊霉素和总球囊霉素相关土壤蛋白比值（EE-GRSP/T-GRSP）以及易提取球囊霉素相关土壤蛋白（EE-GRSP）显著正相关，而与亚隔孢壳属（Didymella）和被孢霉属（Mortierella）相对丰度显著负相关；小于53 μm粉黏粒质量比例显著降低主要与被孢霉属（Mortierella）、白腐菌属（Phlebia）、黑孢壳属（Melanospora）、Fusicolla、柄孢壳属（Podospora）和亚隔孢壳属（Didymella）相对丰度显著正相关，而与EE-GRSP和/或支顶孢属（Acremonium）、柱霉属（Scytalidium）、外瓶霉属（Exophiala）、EE-GRSP/T-GRSP、MBC显著负相关。因此，土壤团聚体稳定性的变异程度受氮肥施用水平影响。本研究条件下，150 kg?hm-2和190 kg?hm-2施氮水平下的团聚体稳定性超过230 kg?hm-2和270 kg?hm-2施氮水平，与不同施氮量下真菌群落组成及其胶结物质变化显著相关。     

Pseudomonas putida BP25 alters root phenotype and triggers salicylic acid signaling as a feedback loop in regulating endophytic colonization in Arabidopsis thaliana

Endophytic Pseudomonas putida BP25 (PpBP25) triggered density dependent alterations on Arabidopsis thaliana Col-0 growth. Endogenous colonization of PpBP25 was found regulated within Arabidopsis that caused induction and repression of 131 and 74 plant genes, respectively. Induced genes like WRKY33, AtRLP19, ATL2, ATEXO70B2, pEARLI, RPS2, CBP60G, PLA2, CRK18, ATFBS1, DREB2A, TIR, RAP2.4, and MOS1 were components of defense and salicylic acid (SA) signaling. Development associated genes were found significantly repressed. Biased activation of phytohormone signaling with their associated fitness costs on plant growth was observed. The data suggests that PpBP25 colonization triggered expression of defense genes that restricted its own population in a feedback loop besides causing altered root phenotype.     

Tree cavities in forests - The broad distribution pattern of a keystone structure for biodiversity

We explored the main factors affecting the global distribution of tree cavities - a habitat component of mostly biotic origin that is crucial for many animal species. We considered the influence of eight environmental variables (ranging from the single-tree to the biogeographic-region scale) on cavity density in a meta-analysis of 103 published studies. The global median density of cavities was 16 ha⁻¹, with densities highest in Australasia and lowest in the Palaearctic region. Two major factors influencing density were identified: cavity density was positively related to the amount of precipitation, and was higher in natural than in managed forests. These effects suggest that the distribution of tree cavities largely reflects the incidence of fungal heart-rot in trees, and that forest management, by affecting wood decay processes, can have a broad-scale impact on tree microhabitat availability. Although air temperature, forest composition and wood hardness had suggestive univariate effects, neither these variables nor biogeographic region explained any additional variation in multifactor models. In regions where woodpeckers are present there was an upper limit to the density of woodpecker-excavated cavities (approximately 10-20 cavities ha⁻¹) that was considerably lower than the highest total cavity densities encountered (up to 140 ha⁻¹). This indicates that primary cavity-nesters are particularly important keystone species in cavity-poor forests where wood decay processes are suppressed either climatically or by forest management.     

Fatty acid composition of various ectomycorrhizal fungi and ectomycorrhizas of Norway spruce

Whole cell fatty acid (WCFA) compositions of three different structures of ectomycorrhizal (ECM) fungi: sporocarps, pure culture mycelia and ectomycorrhizas were analysed to evaluate the potential use of fatty acid profiles as biomarkers for ECM fungi and ectomycorrhiza-associated bacteria. Sporocarps of Amanita muscaria, Amanita rubescens, Lactarius rufus, Lactarius thejogalus, Leccinum scabrum, Paxillus involutus, Russula foetens, Russula rosea, Russula vesca, Suillus grevillei, Tylopilus felleus, Xerocomus badius, Xerocomus subtomentosus, pure cultures of A. muscaria, P. involutus, X. badius, X. subtomentosus, Suillus bovinus Suillus luteus and seven ectomycorrhizal morphotypes of Norway spruce were examined. Our results revealed species-specific composition of fatty acids of fungal sporocarps and pure culture mycelia. Ectomycorrhizal morphotypes distinguished and identified by morphological and molecular methods (PCR-RLFP and sequencing) created specific fatty acid profiles. The dominating fatty acids in pure cultures and sporocarps were 18:2ω6,9, 18:1ω9 and 16:0, whereas ectomycorrhizas also contained plant and bacterial specific fatty acids. Especially, fatty acids specific to Gram-positive bacteria 15:0 anteiso and 17:0 anteiso were present in relatively high amounts and suggested that these bacteria are dominating in the examined Norway spruce mycorrhizosphere. In conclusion, our results show that fatty acid based methods can be useful in studies of ectomycorrhizal fungi, both as a quick method for differentiation of fungal species and also in studies of mycorrhiza-associated microorganisms in the field.     

Infection and colonization of aseptically micropropagated sugarcane seedlings by nitrogen-fixing endophytic bacterium, Herbaspirillum sp. B501gfp1

In this study, we used Herbaspirillum sp. B501gfp1 (B501gfp1), an isolate from wild rice, to investigate the interaction between a non-host nitrogen-fixing endophytic bacterium and micropropagated sugarcane plants under aseptic condition. Two Japanese sugarcane plants (Saccharum sp.) cultivars (cvs) NiF8 and Ni15 were inoculated using B501gfp1 in two inoculum doses of 10⁸ and 10² bacterial-cells-per-milliliter suspension. The results showed that bacterial cells colonized both the root and stem tissues, and colonization was apparent in the intercellular spaces. Higher bacterial numbers were detected in plant tissues inoculated with the higher inoculum concentration treatment. Bacterial numbers also varied between the two cultivars, with the higher values determined in cv Ni15. This study provides evidence that Herbaspirillum sp. B501gfp1, a rice isolate, could colonize sugarcane tissues, suggesting non-specificity of host plant among endophytes.