scholarly journals Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Hyun Kim ◽  
Yong-Hwan Lee

Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.

2021 ◽  
Author(s):  
Lindsay Todman ◽  
Andrew Neal

<p>Soil microbial communities (microbiomes) are dynamic, responding continually to their surrounding environment.  These dynamics may relate to changes in the taxonomic/phylogenetic community structure as well as the functional capacity of the entire microbiome. This dynamism makes it challenging to define resilience for such ecosystems. Here, resilient communities are those able to adjust their taxonomic composition under environmental pulse or press stresses to maintain or restore a particular function.  Trait-based models typically assume trade-offs between life cycle strategies because of the resources required to enable different behaviours. An individual trait may be advantageous depending on the environmental conditions at a particular time and location. However, recent experiments addressing resilience in which soils were repeatedly exposed to stress cycles show soils developed the ability to maintain function despite a repeatedly imposed pulse stress. This suggests that a stress tolerance strategy operates in conjunction with other life cycle strategies. Here, we consider conceptual approaches to reconcile these findings – such as the inclusion of additional life strategies to represent further dimensions of soil community function and a community level trait-based approach that represents the dynamics of functional change in trait space. We also consider the challenge, pertinent to resilience modelling, of distinguishing between stress tolerance and the exposure to stress in heterogeneous soil; both aspects will affect the soil microbial community response, yet the latter could erroneously affect stress tolerance parameters in a trait-based model.</p>


2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Wei Zhuang ◽  
Xiaoli Yu ◽  
Ruiwen Hu ◽  
Zhiwen Luo ◽  
Xingyu Liu ◽  
...  

AbstractMangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56–74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.


PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244682
Author(s):  
Martino Adamo ◽  
Samuele Voyron ◽  
Matteo Chialva ◽  
Roland Marmeisse ◽  
Mariangela Girlanda

In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.


Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3833
Author(s):  
Fatma M. Elessawy ◽  
Albert Vandenberg ◽  
Anas El-Aneed ◽  
Randy W. Purves

Pulse crop seed coats are a sustainable source of antioxidant polyphenols, but are typically treated as low-value products, partly because some polyphenols reduce iron bioavailability in humans. This study correlates antioxidant/iron chelation capabilities of diverse seed coat types from five major pulse crops (common bean, lentil, pea, chickpea and faba bean) with polyphenol composition using mass spectrometry. Untargeted metabolomics was used to identify key differences and a hierarchical analysis revealed that common beans had the most diverse polyphenol profiles among these pulse crops. The highest antioxidant capacities were found in seed coats of black bean and all tannin lentils, followed by maple pea, however, tannin lentils showed much lower iron chelation among these seed coats. Thus, tannin lentils are more desirable sources as natural antioxidants in food applications, whereas black bean and maple pea are more suitable sources for industrial applications. Regardless of pulse crop, proanthocyanidins were primary contributors to antioxidant capacity, and to a lesser extent, anthocyanins and flavan-3-ols, whereas glycosylated flavonols contributed minimally. Higher iron chelation was primarily attributed to proanthocyanidin composition, and also myricetin 3-O-glucoside in black bean. Seed coats having proanthocyanidins that are primarily prodelphinidins show higher iron chelation compared with those containing procyanidins and/or propelargonidins.


2020 ◽  
Vol 96 (6) ◽  
Author(s):  
A Katsoula ◽  
S Vasileiadis ◽  
M Sapountzi ◽  
Dimitrios G Karpouzas

ABSTRACT Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant–soil system and agricultural production.


2017 ◽  
Vol 32 (1) ◽  
pp. 11
Author(s):  
IVONNE LUNA ORTEGA ◽  
VICENCIO DE LA CRUZ FRANCISCO

Las macroalgas son abundantes en el arrecife Oro Verde, Veracruz pero, hasta ahora, se desconocía su riqueza taxonómica, y se presume que presentan asentamientos en los corales escleractinios hermatípicos. Por ello el presente trabajo investigó qué especies de corales presentaron colonizaciones algales; además, se determinó la composición taxonómica y la similitud de los ensambles de macroalgas entre las especies de corales escleractinios. Se establecieron diez puntos de muestreo de manera sistemática en el arrecife; en cada lugar de estudio se colocó un transecto de banda de 50 x 2 m para localizar y recolectar macroalgas en superficies muertas de corales escleractinios. La frecuencia de aparición de las algas se estimó con base en el total de corales estudiados, así como para cada especie coral. Para explicar similitudes y diferencias significativas de la composición de ensamblajes macroalgales entre especies de corales se aplicaron análisis de similitud y ordenación. Los corales escleractinios con ensambles de algas fueron Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. De un total de 100 colonias coralinas revisadas se determinaron 32 especies de macroalgas, las cuales están representadas en tres divisiones, 10 órdenes y 15 familias. Las macroalgas corticadas, foliosas corticadas y filamentosas fueron las más representadas en especies. Las algas de mayor frecuencia sobre los corales masivos fueron Laurencia obtusa, Amphiroa rigida y Caulerpa chemnitzia. Los corales masivos con mayor número de registros de algas fueron S. siderea (9 especies), M. cavernosa (19) y P. strigosa (17). Los ensambles algales en los corales masivos presentaron baja similitud, sin embargo no se detectaron grupos significativamente disimiles. Solamente S. siderea y M. cavernosa son ligeramente parecidos en la composición ficológica. Los resultados sugieren que los corales masivos del arrecife Oro Verde son vulnerables a la colonización de algas, pero es necesario indagar qué condiciones preceden al asentamiento algal.Macroalgal assemblages on dead surfaces of scleractinian corals (Anthozoa: Scleractinia) in the Oro Verde reef, Veracruz, MexicoBenthic macroalgae are abundant in the Oro Verde reef but their taxonomic richness was hitherto unknown and it is presumed to present settlements on the massive corals. For this reason, the present work investigated which species of massive corals show algal colonization. Also, their taxonomic composition was determined, and the similarity of the algal assemblages between species of scleractinian corals was measured. Ten sampling points were systematically established in the reef, where a transect band of 50 x 2 m at each site was placed to locate and collect algae fron the dead surfaces of scleractinian corals. The frequency of occurrence of algae species was estimated based on the total number of coral species studied, as well as on each coral species. Similarity and ordination analysis were applied in order to explain similarities and significant differences of the phycological composition among the coral species. Scleractinian corals with algal assemblages were: Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. Thirty-two species of algae were identified from a total of 100 revised coral colonies which are represented in 3 divisions, 10 orders and 15 families. The corticated, foliose corticated and filamentous macroalgae were the most represented species. The most frequent algae on massive corals were Laurencia obtusa, Amphiroa rigida and Caulerpa chemnitzia. Massive corals with higher algal records were S. siderea (9 species), M. cavernosa (19 species) and P. strigosa (17 species). The algal assemblages on the massive corals presented low similarity. However, no significant dissimilar groups were detected. Only S. siderea and M. cavernosa are relatively similar in phycological composition. The results suggest that the massive corals of the Oro Verde reef are vulnerable to the colonization of algae, but it is necessary to investigate the conditions preceding algal settlement.


2018 ◽  
Vol 10 (10) ◽  
pp. 88 ◽  
Author(s):  
Maya Subedi ◽  
Lope G. Tabil ◽  
Albert Vandenberg

Efficient milling is the key economic trait for the red lentil industry. Various seed characteristics including seed coat color can influence milling characteristics. Four basic seed coat ground colors (green, gray, tan, and brown) of 16 red lentil genotypes from a common genetic background were compared to determine the effect of seed coat color genes on three key milling quality traits: dehulling efficiency (DE), milling recovery (MR), and football recovery (FR). These genotypes were grown at two locations in Saskatchewan, Canada for two years. DE, MR, and FR results varied depending on the seed coat color conferred by specific genotypes. Green and gray seed coat color (homozygous recessive tgc allele) genotypes had significantly higher DE and MR percentages compared to brown or tan seed coat types (homozygous dominant Tgc allele) depending on genotype interaction with site-year. Seeds with brown or tan seed coats had significantly higher FR percentages in two site-years. Red cotyledon lentils with uniform shape and green or gray seed coat color might be more profitable for millers who wish to maximize DE and MR of red lentil, but brown seed coat color might be preferable in terms of FR.


Author(s):  
Adrian Valdez ◽  
Sergio Covarrubias

The Andes range in Ecuador presents high biodiversity and characteristic altitudinal gradients, which are frequently threatened by deforestation and farming. In particular, forest have developed in the high inter-Andean alley on volcanic soils forming a unique ecoregion. Little is known on the fungal biodiversity of soil in such high Andean gallery forest submitted to strong degradation pressures. Therefore, in this study we evaluated wether the soil mycobiome was associated with altitudinal gradients during the dry season. Three representative locations were selected based on altitude: A (3,309 meters above the sea level, masl), B (3,809 masl) and C (4,409 masl). High performance sequencing (NGS) of the ITS region of ribosomal DNA genes with Illumina technology was used to explore the fungal taxonomic composition in the soil samples. Our results showed changes in the structure of fungal communities in the different locations, related to the relative abundance of Amplicon Sequence Variants (ASV). Higher fungal diversity was related with the altitudinal gradient with average taxa ranging from 675, 626 and 556 ASVs, respectively from location A to C. The results highlight the complexity and diversity of fungal communities in high Andean forest and the need to protect these unique mycobiomes. The findings in this ecosystem of Ecuador will improve our understanding of distribution, diversity, ecology, and biological perspectives for the restoration of terrestrial microbiomes.


Author(s):  
A. S. Timchenko ◽  
A. N. Sorokin ◽  
N. S. Zdravchev ◽  
A. V. F. Ch. Bobrov ◽  
M. S. Romanov

The seed coat anatomy of Wollemia nobilis W. G. Jones, K. D. Hill et J. M. Allen was carried out. In theresult of analysis of transverse sections of seeds the sufficient parenchymatization of seed coats and their differentiationinto three morphogenetic zones – the exotesta, the mesotesta and the endotesta was revealed. Such characters of thespermoderm as differentiation of the mesotesta into several topographic zones, presence of resin cavities in mesotesta, aswell as the participation of both exotesta and mesotesta in making the wing are treated as the archaic ones. The seeds of W.nobilis are of transitional type between exomesotestal and the exotestal type (according to Corner's typology). In generalthe seed coat structure of W. nobilis fits into the divercity of seed coats structure in the family Araucariaceae and is treatedas a progressive type within the family.


2017 ◽  
Author(s):  
Ellard R Hunting ◽  
Henrik Barmentlo ◽  
Maarten Schrama ◽  
Peter van Bodegom ◽  
Yujia Zhai ◽  
...  

Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood. Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM. Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality. Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.


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