scholarly journals Vertical stratification of microbial communities in woody plants

2021 ◽  
Author(s):  
Mohammad Bahram ◽  
Kati Kings ◽  
Mari Pent ◽  
Sergei Polme ◽  
Daniyal Gohar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Assembly ◽  
Boreal Forests ◽  
Fungal Endophytes ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Distribution Patterns ◽  
Fungal Communities ◽  
Spatial Distance ◽  
Related Factors

Bacterial and fungal endophytes form diverse communities and contribute to the performance and health of their host plants. Recent evidence suggests that both host related factors and environmental conditions determine the community structure of plant endophytes. Yet, we know little about their distribution patterns, and underlying community assembly mechanisms across plant compartments. Here we analysed the structure of bacterial and fungal communities associated with tree compartments as well as their underlying soils across 12 tree individuals in boreal forests. We found that the structure of bacterial and fungal communities depends more strongly on the vertical location of tree compartments rather than the locality, species, and individuals of host trees. Microbial communities showed much stronger host specificity in aboveground than belowground compartments. While having lower compartment community variability compared to fungi, bacterial communities were markedly more distinct between below- and aboveground components but not between hosts, reflecting the greater importance of environmental filtering rather than dispersal limitation and host identity in their community assembly. Our data suggest that spatial distance from soil as a major microbiome source contributes to the formation of microbiomes in plants, and that bacterial and fungal communities may follow contrasting assembly processes.

scholarly journals Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Pengfa Li ◽  
Weitao Li ◽  
Alex J. Dumbrell ◽  
Ming Liu ◽  
Guilong Li ◽  
...  
Keyword(s):  
Spatial Variation ◽  
Fungal Community ◽  
Community Assembly ◽  
Soil Depth ◽  
Environmental Filtering ◽  
Its Region ◽  
Dispersal Limitation ◽  
Fungal Communities ◽  
Subtropical China ◽  
Soil Layers

ABSTRACT Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, “everything is everywhere, but the environment selects,” although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths. IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.

scholarly journals Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

2016 ◽  
Vol 13 (10) ◽  
pp. 2901-2911 ◽  
Author(s):  
Torsten Hauffe ◽  
Christian Albrecht ◽  
Thomas Wilke
Keyword(s):  
Community Composition ◽  
Community Assembly ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Species Interaction ◽  
Relative Importance ◽  
Lake Depth ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Speciation Model

Abstract. The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the “metacommunity speciation model”.The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes – environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative – inferring the drivers of biotic evolution – and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

scholarly journals Maternal effects and environmental filtering shape seed fungal communities in oak trees

2019 ◽  
Author(s):  
Tania Fort ◽  
Charlie Pauvert ◽  
Amy E. Zanne ◽  
Otso Ovaskainen ◽  
Thomas Caignard ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Maternal Effects ◽  
Environmental Filtering ◽  
Fungal Communities ◽  
Future Research ◽  
Phenotypic Traits ◽  
List Type ◽  
Elevation Gradients ◽  
Sessile Oak ◽  
Starting Point

SummaryTrees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have received little attention.To unravel these processes, we analyzed the microbial communities of seeds collected in populations of sessile oak (Quercus petraea) growing along elevation gradients. We focused on the fungal communities as this group includes seed pathogens. Ecological processes shaping the communities were quantified using joint species distribution models.Fungi were present in all seed tissues, including the embryo. Fungal communities differed significantly among oak populations along the elevation gradients, and among mother trees within the same population. These maternal effects remained significant after seed fall, despite colonization by fungal species on the ground. Associations between tree pathogens and their antagonists were detected in the seeds.Our results demonstrate that both maternal effects and environmental filtering shape seed microbial communities of sessile oak. They provide a starting point for future research aimed at identifying the seed extended phenotypic traits that influence seed dispersal and germination, and seedling survival and growth across environments.

Differences among regions in environmental predictors of primate community similarity affect conclusions about community assembly

2019 ◽  
Vol 35 (2) ◽  
pp. 83-90 ◽  
Author(s):  
Lydia Beaudrot ◽  
Andrew J. Marshall
Keyword(s):  
Community Assembly ◽  
Environmental Variables ◽  
Geographic Distance ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Community Similarity ◽  
Primate Communities ◽  
Assembly Mechanism ◽  
Primate Community ◽  
Environmental Distance

AbstractUnderstanding why ecological communities contain the species they do is a long-standing question in ecology. Two common mechanisms that affect the species found within communities are dispersal limitation and environmental filtering. Correctly identifying the relative influences of these mechanisms has important consequences for our understanding of community assembly. Here variable selection was used to identify the environmental variables that best predict tropical forest primate community similarity in four biogeographic regions: the Neotropics, Afrotropics, Madagascar and the island of Borneo in South-East Asia. The environmental variables included net primary productivity and altitude, as well as multiple temperature, precipitation and topsoil variables. Using the best environmental variables in each region, Mantel and partial Mantel tests were used to reanalyse data from a previously published study. The proportion of variance explained increased for each region. Despite increases, much of the variation remained unexplained for all regions (R2: Africa = 0.45, South America = 0.16, Madagascar = 0.28, Borneo = 0.10), likely due to different evolutionary and biogeographic histories within each region. Nonetheless, substantial variation among regions in the environmental variables that best predicted primate community similarity were documented. For example, none of the 14 environmental variables was included for all four regions, yet each variable was included for at least one region. Contrary to prior results, environmental filtering was an important assembly mechanism for primate communities in tropical forests worldwide. Geographic distance more strongly predicted African and South American communities whereas environmental distance more strongly predicted Malagasy and Bornean communities. These results suggest that dispersal limitation structures primate communities more strongly than environmental filtering in Africa and in South America whereas environmental filtering structures primate communities more strongly than dispersal limitation in Madagascar and Borneo. For communities defined by genera, environmental distance more strongly predicted primate communities than geographic distance in all four regions, which suggests that environmental filtering is a more influential assembly mechanism at the genus level. Therefore, a more nuanced consideration of environmental variables affects conclusions about the influences of environmental filtering and dispersal limitation on primate community structure.

scholarly journals Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant

2021 ◽  
Vol 12 ◽  
Author(s):  
Guozhuang Zhang ◽  
Guangfei Wei ◽  
Fugang Wei ◽  
Zhongjian Chen ◽  
Mingjun He ◽  
...  
Keyword(s):  
Community Assembly ◽  
Large Scale ◽  
Panax Notoginseng ◽  
Dispersal Limitation ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Biogeographic Patterns ◽  
Ecological Patterns ◽  
Bacteria And Fungi ◽  
Occurrence Patterns

Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area of Panax notoginseng for bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the ‘size-dispersal’ hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota.

scholarly journals Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3454 ◽  
Author(s):  
Amandine Lê Van ◽  
Achim Quaiser ◽  
Marie Duhamel ◽  
Sophie Michon-Coudouel ◽  
Alexis Dufresne ◽  
...  
Keyword(s):  
Community Assembly ◽  
Environmental Filtering ◽  
Functional Trait ◽  
Agrostis Stolonifera ◽  
Fungal Communities ◽  
Plant Host ◽  
Expression Ratio ◽  
Dna And Rna ◽  
Host Effect ◽  
Fungal Microbiome

Background Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. Methods We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the ‘mean expression ratio’, was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg’s K statistic. Results Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The ‘mean expression ratio’ displayed significant but divergent phylogenetic signals between fungal phyla. Discussion These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.

scholarly journals Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Wei Zhuang ◽  
Xiaoli Yu ◽  
Ruiwen Hu ◽  
Zhiwen Luo ◽  
Xingyu Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Fungal Community ◽  
Distribution Patterns ◽  
Niche Differentiation ◽  
Fungal Communities ◽  
Fine Scale ◽  
Fungal Community Structure ◽  
Mangrove Root ◽  
Mangrove Roots ◽  
Metagenome Sequencing

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.

scholarly journals Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Keshao Liu ◽  
Yongqin Liu ◽  
Anyi Hu ◽  
Feng Wang ◽  
Yuying Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Dispersal Ability ◽  
Similar Distribution ◽  
The Tibetan Plateau ◽  
Biogeographic Patterns ◽  
Geographic Patterns ◽  
Related Process

ABSTRACT Geographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.

scholarly journals Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves

2011 ◽  
Vol 279 (1735) ◽  
pp. 1993-2002 ◽  
Author(s):  
Craig R. McClain ◽  
James C. Stegen ◽  
Allen H. Hurlbert
Keyword(s):  
Deep Sea ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Environmental Variable ◽  
Distance Decay ◽  
Spatial Distance ◽  
Explanatory Variables ◽  
Faunal Turnover ◽  
Theoretical Predictions ◽  
Rates Of Decay

Patterns of beta-diversity or distance decay at oceanic scales are completely unknown for deep-sea communities. Even when appropriate data exist, methodological problems have made it difficult to discern the relative roles of environmental filtering and dispersal limitation for generating faunal turnover patterns. Here, we combine a spatially extensive dataset on deep-sea bivalves with a model incorporating ecological dynamics and shared evolutionary history to quantify the effects of environmental filtering and dispersal limitation. Both the model and empirical data are used to relate functional, taxonomic and phylogenetic similarity between communities to environmental and spatial distances separating them for 270 sites across the Atlantic Ocean. This study represents the first ocean-wide analysis examining distance decay as a function of a broad suite of explanatory variables. We find that both strong environmental filtering and dispersal limitation drive turnover in taxonomic, functional and phylogenetic composition in deep-sea bivalves, explaining 26 per cent, 34 per cent and 9 per cent of the variation, respectively. This contrasts with previous suggestions that dispersal is not limiting in broad-scale biogeographic and biodiversity patterning in marine systems. However, rates of decay in similarity with environmental distance were eightfold to 44-fold steeper than with spatial distance. Energy availability is the most influential environmental variable evaluated, accounting for 3.9 per cent, 9.4 per cent and 22.3 per cent of the variation in functional, phylogenetic and taxonomic similarity, respectively. Comparing empirical patterns with process-based theoretical predictions provided quantitative estimates of dispersal limitation and niche breadth, indicating that 95 per cent of deep-sea bivalve propagules will be able to persist in environments that deviate from their optimum by up to 2.1 g m −2 yr −1 and typically disperse 749 km from their natal site.

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