scholarly journals Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume

2020 ◽  
Author(s):  
Josep Ramoneda ◽  
Jaco Le Roux ◽  
Emmanuel Frossard ◽  
Beat Frey ◽  
Hannes Andres Gamper
Keyword(s):  
Community Assembly ◽  
Root Nodule ◽  
Regional Scale ◽  
Dispersal Limitation ◽  
System Size ◽  
Community Diversity ◽  
Plant Performance ◽  
Soil Conditions ◽  
Ecological Processes ◽  
Rhizobial Diversity

AbstractUnderstanding how plant-associated microbial communities assemble and the roles they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, assemblages are mostly determined by filtering by the host as well as abiotic soil conditions. However, for legumes adapted to highly variable environments and nutrient-poor soils, filtering out rhizobial partners may not be an effective strategy to ensure symbiotic benefits. As a consequence, this can lead to net increases in rhizobial diversity driven by stochastic (neutral) assembly processes. Here, we addressed whether symbiotic promiscuity of rooibos (Aspalathus linearis Burm. Dahlgren), reflects increases in rhizobial diversity that are independent of the environmental conditions, following a neutral assembly. We performed a common garden experiment to assess whether root system size and location- and habitat-specific rhizobial propagule pools of rooibos affected rhizobial community diversity and composition. We found a dominance of drift in driving taxonomic turnover in the root nodule communities, but operating at different scales in the dominant Mesorhizobium symbionts and the rest of bacterial taxa. Specifically, drift triggered differentiation between the core rhizobial symbionts of rooibos due to dispersal limitation on a regional scale, whereas it dominated the assembly of non-dominant rhizobial taxa at the root level. This suggests the existence of a significant neutral component in rhizobial community assembly when selectivity by the host plant is low. We conclude that in this promiscuous legume neutral processes govern bacterial community root nodule community assembly, but that these operate at different scales in dominant and rare rhizobial symbionts of the plant.

scholarly journals Stochastic and deterministic drivers of seasonal variation of fungal community in tobacco field soil

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6962
Author(s):  
Xing Li ◽  
Tianming Li ◽  
Delong Meng ◽  
Tianbo Liu ◽  
Yongjun Liu ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Fungal Community ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Null Model ◽  
Dispersal Limitation ◽  
Community Diversity ◽  
Ecological Processes ◽  
Soil Fungal Community ◽  
Community Variation

Background The soil fungal community plays an important role in global carbon cycling and shows obvious seasonal variations, however, drivers, particularly stochastic drivers, of the seasonal variation in the fungal community have never been addressed in sufficient detail. Methods We investigated the soil fungal community variation between summer growing (SG) and winter fallow (WF) stage, through high throughput sequencing of internal transcribed spacer (ITS) amplicons. Subsequently, we assessed the contribution of different ecological processes to community assembly using null-model-based statistical framework. Results The results showed that the fungal community diversity decreased significantly after tobacco cropping in the SG stage and the composition showed a clear turnover between the WF and SG stages. The variation in community composition was largely attributable to the presence of a small portion of Dothideomycetes in the WF stage that dominated the soil fungal community in the SG stage. The organic matter, temperature, and water content were the main deterministic factors that regulated the fungal community; these factors explained 34.02% of the fungal community variation. Together with the result that the fungal community was mainly assembled by the dispersal process, our results suggested that the stochastic factors played important roles in driving the seasonal variation of fungal community. The dispersal limitation dominated the fungal community assembly during the WF stage when homogenizing dispersal was the main assembly process of the fungal community in the SG stage. Thus, we proposed that the dispersal processes are important drivers for seasonal variation of fungal community in tobacco planted soil.

scholarly journals Dispersal Limitation Expands the Diversity of Coral Microbiome Metacommunity in the South China Sea

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiandong Zhang ◽  
Anyi Hu ◽  
Yingting Sun ◽  
Qingsong Yang ◽  
Junde Dong ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Community Assembly ◽  
Dispersal Limitation ◽  
The South China Sea ◽  
The South ◽  
Ecological Processes ◽  
Core Microbiome ◽  
China Sea ◽  
Coral Microbiome

The coral microbiome is one of the most complex microbial biospheres. However, the ecological processes shaping coral microbiome community assembly are not well understood. Here, we investigated the abundance, diversity, and community assembly mechanisms of coral-associated microbes from a highly diverse coral metacommunity in the South China Sea. Compared to seawater, the coral microbial metacommunity were defined by highly variable bacterial abundances among individual coral samples, high species evenness but not high species richness, high β-diversity, and a small core microbiome. We used variation partitioning analysis, neutral community model, and null model to disentangle the influences of different ecological processes in coral microbiome assembly. Measured physico-chemical parameters of the surrounding seawater and the spatial factor together explained very little of the variation in coral microbiome composition. Neutral processes only explained a minor component of the variation of coral microbial communities, suggesting a non-stochastic community assembly. Homogeneous and heterogeneous selection, but not dispersal, contributed greatly to the assembly of the coral microbiome. Such selection could be attributed to the within-host environments rather than the local environments. Our results demonstrated that dispersal limitation and host filtering contribute significantly to the assembly of discrete coral microbial regimes and expand the metacommunity diversity.

scholarly journals Stochastic Community Assembly: Does It Matter in Microbial Ecology?

2017 ◽  
Vol 81 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Daliang Ning
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Ecology ◽  
Community Assembly ◽  
Community Diversity ◽  
Ecological Processes ◽  
Experimental Approaches ◽  
Deterministic Processes ◽  
Deterministic Components ◽  
Microbial Community Assembly

SUMMARY Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

scholarly journals Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach

2020 ◽  
Author(s):  
Josep Ramoneda ◽  
Jaco Le Roux ◽  
Emmanuel Frossard ◽  
Beat Frey ◽  
Hannes Andres Gamper
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Root Nodule ◽  
Plant Traits ◽  
Dispersal Limitation ◽  
Soil Conditions ◽  
Plant Host ◽  
Legume Crop ◽  
Population Type ◽  
Prediction Approach

AbstractThere is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread Mesorhizobium ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.

scholarly journals Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Josep Ramoneda ◽  
Johannes J Le Roux ◽  
Emmanuel Frossard ◽  
Beat Frey ◽  
Hannes Andres Gamper
Keyword(s):  
Bacterial Communities ◽  
Root Nodules ◽  
Dispersal Limitation ◽  
Geographic Area ◽  
Plant Performance ◽  
Host Plant Selection ◽  
Soil Conditions ◽  
Legume Crop ◽  
Noda Gene ◽  
Ecological Drift

ABSTRACT Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.

scholarly journals Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil

2021 ◽  
Vol 7 (8) ◽  
pp. 587
Author(s):  
Danielle Hamae Yamauchi ◽  
Hans Garcia Garces ◽  
Marcus de Melo Teixeira ◽  
Gabriel Fellipe Barros Rodrigues ◽  
Leila Sabrina Ullmann ◽  
...  
Keyword(s):  
Fungal Community ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Deciduous Forest ◽  
Regional Scale ◽  
Southeastern Brazil ◽  
Transitional Region ◽  
Illumina Platform ◽  
Ecological Processes ◽  
Life On Earth

Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls’ and armadillos’ burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls’ burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities’ structures.

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 Phyllosphere community assembly and response to drought stress on common tropical and temperate forage grasses

2021 ◽  
Author(s):  
Emily K. Bechtold ◽  
Stephanie Ryan ◽  
Sarah E. Moughan ◽  
Ravi Ranjan ◽  
Klaus Nüsslein
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Bacterial Community ◽  
Community Assembly ◽  
Community Diversity ◽  
Grass Species ◽  
Severe Drought ◽  
Hormone Production ◽  
Plant Host ◽  
Bacterial Community Diversity

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future.

scholarly journals Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

2018 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Caterina. R. Giner ◽  
Anders K. Krabberød ◽  
Thomas S. B. Schmidt ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Sequence Data ◽  
Scale Effects ◽  
Dispersal Limitation ◽  
Global Scale ◽  
Global Ocean ◽  
Ecosystem Functions ◽  
Ecological Processes ◽  
Surface Ocean

ABSTRACTThe smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts thatselection,dispersalanddriftare main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.SIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmentalselection,dispersaland random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

scholarly journals Climate changes in mangrove forests and salt marshes

2016 ◽  
Vol 64 (spe2) ◽  
pp. 37-52 ◽  
Author(s):  
Yara Schaeffer-Novelli ◽  
Eduardo Juan Soriano-Sierra ◽  
Claudia Câmara do Vale ◽  
Elaine Bernini ◽  
André Scarlate Rovai ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Early Warning ◽  
Salt Marshes ◽  
Regional Scale ◽  
Level Energy ◽  
Mangrove Forests ◽  
Coastal Zones ◽  
Coastal Habitat ◽  
Ecological Processes ◽  
Salt Marsh Species

Abstract This synthesis is framed within the scope of the Brazilian Benthic Coastal Habitat Monitoring Network (ReBentos WG 4: Mangroves and Salt Marshes), focusing on papers that examine biodiversity-climate interactions as well as human-induced factors including those that decrease systemic resilience. The goal is to assess difficulties related to the detection of climate and early warning signals from monitoring data. We also explored ways to circumvent some of the obstacles identified. Exposure and sensitivity of mangrove and salt marsh species and ecosystems make them extremely vulnerable to environmental impacts and potential indicators of sea level and climate-driven environmental change. However, the interpretation of shifts in mangroves and salt marsh species and systemic attributes must be scrutinized considering local and setting-level energy signature changes; including disturbance regime and local stressors, since these vary widely on a regional scale. The potential for adaptation and survival in response to climate change depends, in addition to the inherent properties of species, on contextual processes at the local, landscape, and regional levels that support resilience. Regardless of stressor type, because of the convergence of social and ecological processes, coastal zones should be targeted for anticipatory action to reduce risks and to integrate these ecosystems into adaptation strategies. Management must be grounded on proactive mitigation and collaborative action based on long-term ecosystem-based studies and well-designed monitoring programs that can 1) provide real-time early warning and 2) close the gap between simple correlations that provide weak inferences and process-based approaches that can yield increasingly reliable attribution and improved levels of anticipation.

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