scholarly journals Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nittay Meroz ◽  
Nesli Tovi ◽  
Yael Sorokin ◽  
Jonathan Friedman
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Knowledge Gap ◽  
Assembly Rules ◽  
Bottom Up ◽  
Ecological Equilibrium ◽  
Simple Assembly

AbstractManaging and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities, with 3–18 replicates each, for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach—changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities.

scholarly journals Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales

2020 ◽  
Author(s):  
Nittay Meroz ◽  
Nesli Tovi ◽  
Yael Sorokin ◽  
Jonathan Friedman
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Knowledge Gap ◽  
Assembly Rules ◽  
Bottom Up ◽  
Ecological Equilibrium ◽  
Simple Assembly

AbstractManaging and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach - changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities.

scholarly journals Rhizosphere bacterial community composition depends on plant diversity legacy in soil and plant species identity

2018 ◽  
Author(s):  
Marc W. Schmid ◽  
Terhi Hahl ◽  
Sofia J. van Moorsel ◽  
Cameron Wagg ◽  
Gerlinde B. De Deyn ◽  
...  
Keyword(s):  
Species Diversity ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Plant Diversity ◽  
Bacterial Communities ◽  
Biodiversity Loss ◽  
Plant Species Diversity ◽  
Species Identity ◽  
Soil Biodiversity

AbstractSoil microbes are known to be involved in a number of essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this timeframe plants with a monoculture or mixture history changed in the microbial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same monocultures or mixtures (monoculture- or mixture-type plants) in pots inoculated with microbes extracted from the monoculture and mixture soils. After five months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S-rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Microbial community structure in the plant rhizosphere was primarily determined by soil legacy (monoculture vs. mixture soil) and by plant species identity, but not by plant legacy (monoculture- vs. mixture-type plants). In seven out of the eight plant species bacterial abundance was larger when inoculated with microbes from mixture soil. We conclude that plant diversity can strongly affect belowground community composition and diversity, feeding back to the assemblage of rhizosphere microbial communities in newly establishing plants. Thereby our work demonstrates that concerns for plant biodiversity loss are also concerns for soil biodiversity loss.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

scholarly journals Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4735 ◽  
Author(s):  
Angus Angermeyer ◽  
Sarah C. Crosby ◽  
Julie A. Huber
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Latitudinal Gradient ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Environmental Selection

Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

scholarly journals Productive bacterial communities exclude invaders

2019 ◽  
Author(s):  
Matt L. Jones ◽  
Damian W. Rivett ◽  
Alberto Pascual-García ◽  
Thomas Bell
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Invasion Success ◽  
Limiting Factors ◽  
Community Respiration ◽  
Invasion Resistance ◽  
Microbial Invasion ◽  
Community Growth

AbstractExperiments with artificial microbial communities indicate that certain community compositions are more resistant to microbial invasion than others. However, few invasion experiments have used natural microbial communities to investigate how the effect of community composition on invasion resistance relates to different aspects of community growth. We conducted experimental invasions of two bacterial species (Pseudomonas fluorescens and Pseudomonas putida) into 678 bacterial communities, comparing composition to several aspects of community growth prior to invasion to see how well they predicted invasion. We show that even in these complex microbial assemblages, the effects of resident community composition and growth are largely overlapping - with parameters associated with the productivity of the community (cell yield, community respiration) emerging as the main limiting factors for invasion success. Despite their complexity, these communities can be classified into a few compositional groups that are associated with the main differences in community growth, and thereby invasion resistance.

Weed seed mortality in soils with contrasting agricultural management histories

Weed Science ◽  
2006 ◽  
Vol 54 (02) ◽  
pp. 291-297 ◽  
Author(s):  
Adam S. Davis ◽  
Kathleen I. Anderson ◽  
Steven G. Hallett ◽  
Karen A. Renner
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Weed Seed ◽  
Soil Microbial ◽  
Giant Foxtail ◽  
Seed Mortality

It has been proposed that cropping systems can be managed to promote the development of soil microbial communities that accelerate weed seed mortality. We examined soil fungal and bacterial communities, soil C:N ratio, soil particle size fractions, and weed seed mortality in soil from fields with over 10 yr of five contrasting management histories with the objective of determining if seed mortality could be explained by differences in soil properties. Seed mortality of giant foxtail and velvetleaf were greatest in soil from the conventionally managed systems and lowest in soil from a reduced input system. Principal-components analysis of soil microbial communities, as determined through denaturing gradient gel electrophoresis of polymerase chain reaction–amplified ribosomal RNA genes (PCR-DGGE), showed distinct differences in the composition of fungal and bacterial communities among the study soils. The first principal component of the 18S rDNA PCR-DGGE analysis of fungal community composition showed a strong negative correlation with both giant foxtail (− 0.52, P < 0.05) and velvetleaf (− 0.57, P < 0.01) seed mortality, as did ordination with nonmetric multidimensional scaling (NMS) [giant foxtail (− 0.54, P < 0.01) and velvetleaf (− 0.60, P < 0.01)], suggesting that seeds of the two species were affected similarly by changes in the soil fungal community. For giant foxtail, weed seed mortality was also positively correlated (r = 0.48, P < 0.05) with the first NMS axis of the bacterial 16S rDNA analysis. None of the other measured soil properties were significantly correlated with weed seed mortality. Thus, for the soils tested here, management history, microbial community composition, and weed seed mortality were linked. To extend these results to the field, more work is needed to identify components of the fungal and bacterial communities that are active in seed degradation, and to develop conservation biocontrol recommendations for these species.

scholarly journals Differential impact of top-down and bottom-up forces in structuring freshwater bacterial communities

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
A S Pradeep Ram ◽  
J Keshri ◽  
T Sime-Ngando
Keyword(s):  
Nucleic Acid ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Host Community ◽  
Heterotrophic Nanoflagellates ◽  
Rrna Gene ◽  
Top Down ◽  
Bottom Up ◽  
Host Diversity

ABSTRACT Limited data exist on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of classes Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces, thereby resulting in differences (P < 0.001) in bacterial community composition and diversity, as observed from analysis of similarities and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (P < 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth-limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of ‘killing the winner’, where the availability of growth-limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity.

scholarly journals Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7356
Author(s):  
Yan Bai ◽  
Xiying Huang ◽  
Xiangrui Zhou ◽  
Quanju Xiang ◽  
Ke Zhao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Primary Succession ◽  
Abiotic Factors ◽  
Bacterial Community Composition ◽  
Living Environment ◽  
Available Phosphorus ◽  
The Tibetan Plateau ◽  
Successional Stages

Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).

Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil

2021 ◽  
Vol 156 ◽  
pp. 108186
Author(s):  
Rasit Asiloglu ◽  
Kobayashi Kenya ◽  
Solomon Oloruntoba Samuel ◽  
Bahar Sevilir ◽  
Jun Murase ◽  
...  
Keyword(s):  
Paddy Field ◽  
Bacterial Communities ◽  
Field Soil ◽  
Top Down ◽  
Bottom Up ◽  
Paddy Field Soil

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

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