Adult plants facilitate their conspecific seedlings by enhancing arbuscular mycorrhizae in a saline soil

Aims

We tested the hypothesis that adult plants can help their conspecific (i.e. an organism belonging to the same species as another organism) seedlings develop symbiosis with arbuscular mycorrhizal fungi (AMF), thereby increasing seedling nutrient uptake and growth in a saline soil.

Methods

Using the halophytic shrub Tamarix chinensis as a model plant, we conducted two field experiments and a greenhouse experiment. Field experiment 1 assessed the importance of below-ground effects of adult neighbor. Field experiment 2 determined the involvement of AMF in neighbor effects by applying fungicide benomyl to obtain AMF suppressed treatment. The greenhouse experiment tested whether neighbor effects were influenced by AMF hyphal connection between adults and seedlings by using 25 μm and 0.45 μm nylon mesh to allow and prevent the AMF hyphae pass through respectively.

Results

Adult neighbor increased shoot biomass and nutrient of target seedlings and the below-ground effects mediated by AMF was facilitative under high soil salinity level. Field experiment 1 showed that adult neighbors reduced soil salinity, increased soil organic matter, and provided AMF spores for target seedlings via whole plant effects or below-ground effects alone. Field experiment 2 showed that shoot biomass and AMF colonization of target seedlings were greater with an adult neighbor when AMF were not suppressed treatment than in AMF were suppressed or there were no neighbors. In the greenhouse experiment, adult neighbors with AMF hyphal connection increased shoot biomass, AMF colonization, and ¹⁵N content of target seedlings under the high salinity level.

Conclusion

The results support our hypothesis that adult plants can promote the growth and nutrient uptake of their conspecific seedlings in a saline soil by helping them to develop AMF symbiosis. These findings highlight the roles of adult neighbor plants on seedlings regeneration through rhizospheric symbiosis in stressful environments.

     

Pine invasion decreases density and changes native tree communities in woodland Cerrado

ABSTRACT

Background: Invasive plants can negatively impact native communities, but the majority of the effects of these invasions have been demonstrated only for temperate ecosystems. Tropical ecosystems, including the Cerrado, a biodiversity hotspot, are known to be invaded by numerous non-native species, but studies of their impacts are largely lacking.

Aims: Our research aimed at quantifying how Pinus spp. presence and density affected Cerrado plant communities.

Methods: We sampled areas invaded and non-invaded by Pinus spp. to determine if pine invasion affected native tree richness, diversity, evenness, and density. We also evaluated if community composition differed between invaded and non-invaded sites.

Results: We found invaded plots had lower native tree densities than non-invaded plots and that Pinus spp. invasions changed native tree communities by reducing native species abundances.

Conclusion: Invasive pines had negative impacts on the native Cerrado tree community by reducing native plant density and changing species abundances. Reduced density and abundance at early invasion stages can result in reduction in biodiversity in the long term.     

Endophytic and rhizospheric enterobacteria isolated from sugar cane have different potentials for producing plant growth-promoting substances

Background and aims

Endophytic and rhizospheric environments differ in many respects, leading to the presence of different bacterial communities at each site. However, microorganisms such as enterobacteria can be found both within plants and in the surrounding soil. Bacteria must present differences in the traits that affect such environments in order to successfully colonise them. The present study compared the plant growth-promoting potential of diazotrophic enterobacteria isolated from the rhizosphere and from within surface-disinfected plants.

Methods

A total of 46 diazotrophic enterobacterial strains (21 rhizospheric and 25 putatively endophytic) belonging to the Klebsiella and Enterobacter genera, which are prevalent in sugar cane plantations, were isolated from the rhizosphere and from surface-disinfected plants. Their ability to synthesise amino acids using combined nitrogen obtained from nitrogen fixation, and their ability to synthesise indole-3-acetic acid (IAA) were determined by high performance liquid chromatography. Endogenous ethylene production by the bacteria was measured using gas chromatography, and biocontrol of phytopathogenic fungi was determined qualitatively using a dual culture technique.

Results

The putative endophytes released significantly higher amounts of amino acids than the rhizospheric bacteria, whilst the latter produced higher quantities of ethylene and were more actively antagonistic to fungi. Both types of bacteria released similar amounts of IAA.

Conclusion

Endophytic and rhizospheric bacteria differ in their capacity to release plant growth-promoting substances, which may be a reflection of their adaptations and an indication of their potential impact on their natural environment.

     

Trait dynamics of Mediterranean xerophytic shrub communities growing on stabilised inland dunes respond to nutrient and aridity gradients

Background: Understanding the processes that determine community assembly and their dynamics is a central issue in ecology. The analysis of functional diversity can improve our understanding of these dynamics by identifying community assembly processes.

Aims: We studied the effect of environment–community covariations on both functional diversity and functional structure of xerophytic shrub communities for inferring the community assembly processes shaping this vegetation type.

Methods: Functional diversity was quantified using (1) community-weighted mean of the studied traits, (2) functional groups, defined using Ward’s hierarchical agglomerative clustering method and (3) Rao’s quadratic entropy. Relationships between functional diversity and environmental gradients were identified by Spearman correlations and modelled using generalised additive models.

Results: Variations in community composition and functional diversity correlated with soil nutrient availability and aridity. Increasing nutrient availability resulted in both greater average plant height and higher abundance of plants with green photosynthetic organ colour, whereas the abundance of nanophanerophytes increases with aridity.

Conclusions: The species composition and trait structure of the studied Mediterranean xerophytic shrub communities varies along nutrient and aridity gradients. This supports the importance of environmental filters for the local assembly and dynamics of these inland dune communities.     

Food preferences of Shorelarks Eremophila alpestris,Snow Buntings Plectrophenax nivalis and Twites Carduelis flavirostris wintering in the Wadden Sea

Capsule Seeds of plants from lower salt marsh communities are preferred, with insects less important.

Methods Droppings of Shorelarks Eremophila alpestris, Snow Buntings Plectrophenax nivalis and Twites Carduelis flavirostris sampled in the German Wadden Sea were analysed and compared with food abundance to assess preferences.

Results Shorelarks prefer seeds of Salicornia sp., Suaeda maritima, Atriplex sp., Halimione portulacoides and unidentified small grass seeds. Insects are eaten mainly in periods of seed shortage, but are consumed in smaller amounts during the winter. The food composition of Snow Buntings is very similar, but additionally Triglochin maritimum is commonly eaten. Twites are specialized on seeds of Salicornia sp. and Suaeda maritima and rarely ingest other seeds and insects. All seeds consumed were of plants from lower salt marsh communities. Many halophyte seeds, and especially those that birds feed on, are rich in energy. Large seeds and those which need a long handling time are avoided.

Conclusion Changes in the lower salt marshes of the Wadden Sea by embankments and intensified grazing might have been responsible for the rapid population decline from the 1960s to 1980s.     

Scottish Birchwoods and their conservation — a Review

Summary

The communities of vascular plants found in Scottish birch woods are briefly described. Birchwoods originate in a variety of ways which affects their likely value for nature conservation. This is discussed using specific examples. The conservation of birchwoods to meet a variety of objectives is considered.     

Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants

Background and Aims

Recently, the truffle species Tuber lyonii Butters was found to be dominant in ectomycorrhizal (EcM) fungal communities of cultivated pecan (Carya illinoinensis (Wangenh.) K. Koch). Many truffle fungi exhibit the trait of effectively colonizing plant roots via spores. We hypothesized that T. lyonii would be well represented in the spore bank of pecan orchard soils where it is found.

Methods

We used axenically-grown pecan seedlings as trap-plants to bait for EcM associates in soils collected beneath truffle-producing pecan trees. EcM fungi on seedlings were characterized through rDNA sequencing and were compared to EcM communities of adult trees in these orchards.

Results

Tuber lyonii mycorrhizas were well formed on seedlings inoculated with truffle spores, but were limited to just a few of the trap-plants grown in field soils. We compared EcM communities of adult pecan orchard trees to those on trap-plants and found distinct communities on each, with a high degree of similarity at the ordinal but not species level.

Conclusions

Although species of Pezizales are abundant in pecan EcM communities and as propagules in their soil spore banks, only a low level of T. lyonii was detected in soil spore banks beneath orchard trees naturally colonized by T. lyonii. Other factors including land-use history or orchard management may better explain this truffle species presence and abundance in pecan EcM communities.

     

Presidential Address—Some Reflections On The Nature Of Species

Background: Variation in the distribution and abundance of woody plants as consequence of disturbances such as fire may be explained by lineage age.

Aims: We tested whether lowland tropical tree lineages that colonise secondary forests are more late-diverging than clades from old-growth forests, and whether tree phylogenetic beta diversity from old-growth to secondary forests is higher in burned than non-burned secondary forests.

Methods: We sampled tree communities in old-growth forests and in secondary forests with distinct disturbance histories (burned and unburned). We calculated mean family age in each plot, and tested for differences among forest types using ANOVA. A phylogenetic fuzzy-weighting procedure was employed to generate a matrix describing the abundance of tree clades per plot, which was then analysed using a principal coordinate analysis.

Results: Most clades found in old-growth forests were underrepresented in secondary forests, which have been heavily colonised by a single species from a young lineage that is not found in old-growth forests. Phylogenetic beta diversity was higher between unburned secondary forests and old-growth forests than between burned secondary forests and old-growth forests.

Conclusions: The capacity of Neotropical trees to colonise secondary forests and persist after fire disturbance may be related to the age of distinct lineages.     

Measurement of the Girth of Coniferous Trees at Braemar in 1894

ABSTRACT

Background: Plant communities are usually characterised by species composition and abundance, but also underlie a multitude of complex interactions that we have only recently started unveiling. Yet, we are still far from understanding ecological and evolutionary processes shaping the network-level organisation of plant diversity, and to what extent these processes are specific to certain spatial scales or environments.

Aims: Understanding the systemic mechanisms of plant–plant network assembly and their consequences for diversity patterns.

Methods: We review recent methods and results of plant–plant networks.

Results: We synthetize how plant–plant networks can help us to: (a) assess how competition and facilitation may balance each other through the network; (b) analyse the role of plant–plant interactions beyond pairwise competition in structuring plant communities, and (c) forecast the ecological implications of complex species dependencies. We discuss pros and cons, assumptions and limitations of different approaches used for inferring plant–plant networks.

Conclusions: We propose novel opportunities for advancing plant ecology by using ecological networks that encompass different ecological levels and spatio-temporal scales, and incorporate more biological information. Embracing networks of interactions among plants can shed new light on mechanisms driving evolution and ecosystem functioning, helping us to mitigate diversity loss.     

Allelopathic vs. autotoxic potential of a grassland weed—evidence from a seed germination experiment

ABSTRACT

Background: Mechanisms affecting invasiveness of non-indigenous species have received much attention. Few studies have investigated invasions by native plants. Invasive native species such as common ragwort (Jacobaea vulgaris) may become noxious weeds. They challenge farming and nature conservation by outcompeting fodder plants or rare herbs. One mechanism that can result in outcompeting plants is by allelopathy.

Aim: We evaluated the potential of J. vulgaris to suppress germination in common and rare grassland species by allelopathy.

Methods: In a germination chamber experiment, we exposed 22 species and J. vulgaris itself to ragwort leachate. We controlled for osmotic effects by germination tests in mannitol solution and water. We assessed germination percentage—time —synchrony and radicle length.

Results: Leachate reduced germination percentage, germination time, synchrony and radicle length. These effects were similar for J. vulgaris, indicating autotoxicity. Rare species germinated less than common species but were not more sensitive to the phytotoxic effects of J. vulgaris. Restraining effects of the leachate were similar to the mere osmotic effect.

Conclusion: Our results question allelopathy as the main driving mechanism behind J. vulgaris gaining dominance. However, the impact of J. vulgaris might depend on the composition of the invaded plant community due to species-specific effects.     

Meta-network: optimized species-species network analysis for microbial communities

Background

The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need.

Results

Hence, in this work, we propose the Meta-Network framework to lucubrate the microbial communities. Rooted in loose definitions of network (two species co-exist in a certain samples rather than all samples) as well as association rule mining (mining more complex forms of correlations like indirect correlation and mutual information), this framework outperforms other methods in restoring the microbial communities, based on two cohorts of microbial communities: (a) the loose definition strategy is capable to generate more reasonable relationships among species in the species-species co-occurrence network; (b) important species-species co-occurrence patterns could not be identified by other existing approaches, but could successfully generated by association rule mining.

Conclusions

Results have shown that the species-species co-occurrence network we generated are much more informative than those based on traditional methods. Meta-Network has consistently constructed more meaningful networks with biologically important clusters, hubs, and provides a general approach towards deciphering the species-species co-occurrence networks.

     

Spatial patterns of species diversity in sand dune plant communities in Yucatan,Mexico: importance of invasive species for species dominance patterns

Background: Coastal ecosystems in Mexico remain understudied in spite of their ecological, economic and conservation value and are being impacted by human activities along the coast. Knowledge on spatial patterns of plant species distribution that helps preserve these fragile ecosystems is crucial.

Aims: We evaluated differences in species richness, species diversity and species dominance patterns in 16 plant communities as well as the degree to which differences were driven by climatic conditions in sandy dunes in Yucatán. We evaluated the importance of invasive species in mediating patterns of species diversity and species dominance patterns.

Results: We found wide variation in plant species richness, species diversity and species dominance patterns among communities that stems from broad climatic differences along dune systems. Invasive plants represent almost one-third of total species richness and seem to be drastically changing the species dominance patterns in these communities.

Conclusions: Regional climatic differences along the Yucatán north coast seems to be a major driver of plant diversity and species composition. Our findings suggest that invasive plants have successfully colonised and spread along the coast over the past 30 years. Even though invasive species do not alter spatial patterns of species diversity, they are becoming more dominant with potential detrimental consequences for native plants.     

Differences between bacterial associations with two root types of Vicia faba L

Abstract

Differences between various inherent physiological characteristics of lateral roots and of taproots of faba bean plants (Vicia faba L.) have been described in the literature. The question as to whether distinct bacterial communities inhabit each of those root types calls for further investigation. This question was tackled using aeroponically grown plants, i.e., plants that were grown under conditions as homogeneous as possible. Samples of the apical 5 cm of taproots and of lateral roots were compared. Metabolic fingerprints of root bacterial communities were analyzed using the Biolog® assay. Specificity of colonization of the different root types by specific bacterial taxa was examined by the Real-Time Polymerase Chain Reaction (PCR) method. Root bacterial communities produced distinct metabolic fingerprints for each of the two root types. Herbaspirillum spp. were found to be associated with lateral roots but not with taproots both under non-saline and saline (50 mM NaCl) conditions. No significant differences were found in the abundance of bacteria with respect to either root type or salinity. It is concluded that different root types, even within single root systems, differ not only in their physiological traits but also in their bacterial associations. Such associations might have adaptive advantages.     

Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school

Background

The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks.

Results

The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities.

Conclusions

There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.

     

Shoot specific fungal endophytes alter soil phosphorus (P) fractions and potential acid phosphatase activity but do not increase P uptake in tall fescue

Aims

An experiment was performed to test how different fungal endophyte strains influenced tall fescue’s ability to access P from four P sources varying in solubility.

Methods

Novel endophyte infected (AR542E+ or AR584E+), common toxic endophyte infected (CTE+), or endophyte-free (E-) tall fescues were grown for 90 days in acidic soils amended with 30 mg kg^?1 P of potassium dihydrogen phosphate (KH₂PO₄), iron phosphate (FePO₄), aluminum phosphate (AlPO₄), or tricalcium phosphate ((Ca₃(PO₄)₂), respectively.

Results

Phosphorus form strongly influenced plant biomass, P acquisition, agronomic P use efficiency, microbial communities, P fractions. P uptake and vegetative biomass were similar for plants grown with AlPO₄, Ca₃(PO₄)₂, and KH₂PO₄ but greater than in control and FePO₄ soils. Infection with AR542E+ resulted in significantly less shoot biomass than CTE+ and E- varieties; there was no influence of endophyte on root biomass. The biomarker for arbuscular mycorrhizal fungi (AM fungi, 16:1ω5c) was selected as an effective predictor of variations in P uptake and tall fescue biomass. Potential acid phosphatase activity was strongly influenced by endophyte x P form interaction.

Conclusions

Endophyte infection in tall fescue significantly affected the NaOH-extractable inorganic P fraction, but had little detectable influence on soil microbial community structure, root biomass, or P uptake.

     

Obituaries

Background: Although impacts of edge effects on forest ecosystems are well known, their consequences on savannas have rarely been explored.

Aims: To investigate the influence of edge effects on the plant community and microclimate of a cerrado fragment in south-eastern Brazil.

Methods: Several plant community variables (density, basal area, richness and cover by each vegetation layer) and microclimatic variables (light, air temperature and humidity), were measured in 10 transects across a savanna fragment surrounded by exotic grasses, and were used to fit semi-parametric models relating these variables with the distance from the habitat edge.

Results: Differences in microclimate and tree communities were poorly related to distance from the edge. On the other hand, there were detectable edge effects on the ground layer community (i.e. plants less than 50 cm in height). Edges had a negative effect on native plants of this layer (density and richness of all species and cover of native grasses), while favouring invasive grasses.

Conclusions: Unlike reports for edge effects in forest ecosystems, microclimate does not explain changes in this cerrado fragment. The most significant edge effect threatening the conservation of cerrado vegetation is the widespread invasion by African grasses. Starting from the fragment borders, this invasion causes changes in the structure and composition of the native plant community, thus jeopardising the population dynamics and persistence of native species.     

Plant functional strategies and environmental constraints in Mediterranean high mountain grasslands in central Spain

Background: The relationship between plant traits and environmental factors will be of value in understanding of functional strategies that plants have developed to cope with the environmental constraints on plant life in Mediterranean high mountain ecosystems.

Aims: The aims of this study were (1) to explore the variation in plant traits in relation to environmental variability; (2) to analyse the functional strategies of species; and (3) to assess the habitat constraints for the species in the study area.

Methods: We sampled the floristic composition of 76 1 m?×?1 m plots on five summits over 2,100 m above sea level in the mountains of the Sistema Central, Spain. Soil properties and temperature and grazing disturbance parameters were recorded. Eight plant traits were assessed in 21 species. Environmental variability and the co-variation of functional traits were analysed by RDA and PCA, respectively. Plant traits and environmental variability were related using fourth-corner analysis.

Results: Traits related to resource acquisition, such as leaf size and N concentration, varied with soil temperature and estimated summer water availability. Leaf dry matter content was found to be related to estimated water availability and soil pH. Seed mass was a factor of snow cover duration and water availability, and clonality to the duration of the vegetative period and estimated water availability. Grazing disturbance was related to the mean plant height of the species.

Conclusions: The results suggest that low temperatures, rather than water shortage, may be the principal limiting factor for resource acquisition in plants. Nevertheless species establishment is limited by water shortage during summer in these Mediterranean high mountain communities.     

Acrolein-detoxifying isozymes of glutathione transferase in plants

Main conclusion

Acrolein is a lipid-derived highly reactive aldehyde, mediating oxidative signal and damage in plants. We found acrolein-scavenging glutathione transferase activity in plants and purified a low K _M isozyme from spinach.

Various environmental stressors on plants cause the generation of acrolein, a highly toxic aldehyde produced from lipid peroxides, via the promotion of the formation of reactive oxygen species, which oxidize membrane lipids. In mammals, acrolein is scavenged by glutathione transferase (GST; EC 2.5.1.18) isozymes of Alpha, Pi, and Mu classes, but plants lack these GST classes. We detected the acrolein-scavenging GST activity in four species of plants, and purified an isozyme showing this activity from spinach (Spinacia oleracea L.) leaves. The isozyme (GST-Acr), obtained after an affinity chromatography and two ion exchange chromatography steps, showed the K _M value for acrolein 93 μM, the smallest value known for acrolein-detoxifying enzymes in plants. Peptide sequence homology search revealed that GST-Acr belongs to the GST Tau, a plant-specific class. The Arabidopsis thaliana GST Tau19, which has the closest sequence similar to spinach GST-Acr, also showed a high catalytic efficiency for acrolein. These results suggest that GST plays as a scavenger for acrolein in plants.

     

ENIGMA: an enterotype-like unigram mixture model for microbial association analysis

Background

One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as “enterotype”, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease.

Results

We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease.

Conclusion

In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson’s disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).