scholarly journals Direct quantification of ecological drift at the population level in synthetic bacterial communities

2020 ◽  
Vol 15 (1) ◽  
pp. 55-66
Author(s):  
Stilianos Fodelianakis ◽  
Adriana Valenzuela-Cuevas ◽  
Alan Barozzi ◽  
Daniele Daffonchio
Keyword(s):  
Bacterial Communities ◽  
Population Level ◽  
Species Loss ◽  
Controlled Experiments ◽  
Ecological Processes ◽  
Β Diversity ◽  
High Selection ◽  
Experimental Findings ◽  
Ecological Drift ◽  
Direct Quantification

AbstractIn community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4–2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to ~5% of species loss and to ~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.

scholarly journals Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Pei Wang ◽  
Xiao Kong ◽  
Hongsong Chen ◽  
Youlun Xiao ◽  
Huijun Liu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Microbial Network ◽  
Β Diversity ◽  
Group I ◽  
Α Diversity ◽  
Microbe Interactions ◽  
Endophytic Bacterial Community ◽  
Group Ii

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

scholarly journals A game theory model for gut bacterial nutrient utilization strategies during human infancy

2020 ◽  
Vol 287 (1931) ◽  
pp. 20200824 ◽  
Author(s):  
Inga Leena Angell ◽  
Knut Rudi
Keyword(s):  
Game Theory ◽  
Gut Microbiota ◽  
Nutrient Utilization ◽  
Theory Model ◽  
Ecological Processes ◽  
Β Diversity ◽  
Gut Colonization ◽  
Α Diversity ◽  
Colonization Patterns ◽  
Expanding Population

Despite the fact that infant gut colonization patterns have been extensively studied, we have limited knowledge about the underlying ecological processes. This particularly relates to the ecological choice of nutrient utilization strategies. The aim of the current study was therefore to compare empirically determined nutrient utilization strategies with that expected from a combinatorial game theory model. Observational analyses for 100 mother–child pairs suggested mother–child transmission of specialists with the potential to use few nutrients. Generalists, on the other hand, with the potential to use many nutrients, peaked at three months of age for the children. The level of generalists was gradually replaced with specialists up to 12 months of age. Game theory simulation revealed a competitive advantage of generalists in an expanding population, while more specialized bacteria were favoured with the maturation of the population. This suggests that the observed increase in generalists in the three-month-old children could be due to an immature, expanding gut microbiota population while the increase of specialists at 12 months could be due to population maturation. The simulated and empirical data also correspond with respect to an increased α diversity and a decreased β diversity with the number of simulations and age, respectively. Taken together, game theory simulation of nutrient utilization strategies can therefore provide novel insight into the maturation of the human gut microbiota during infancy.

scholarly journals Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Ragnhild I Vestrum ◽  
Kari J K Attramadal ◽  
Olav Vadstein ◽  
Madeleine Stenshorne Gundersen ◽  
Ingrid Bakke
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Atlantic Cod ◽  
Animal Health ◽  
Striking Difference ◽  
Ecological Processes ◽  
Opportunistic Bacteria ◽  
Atlantic Cod Larvae ◽  
Microbe Interactions ◽  
Host Microbe Interactions

ABSTRACT Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival.

scholarly journals Bacterial colonization and succession in a newly opened hospital

2017 ◽  
Vol 9 (391) ◽  
pp. eaah6500 ◽  
Author(s):  
Simon Lax ◽  
Naseer Sangwan ◽  
Daniel Smith ◽  
Peter Larsen ◽  
Kim M. Handley ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Bacterial Colonization ◽  
Dynamic Bayesian Network ◽  
Hospital Staff ◽  
Hospital Environment ◽  
Temporal Correlations ◽  
Β Diversity ◽  
Bacterial Dynamics ◽  
Surgical Recovery

The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient’s stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes ofStaphylococcusandPropionibacteriumwere identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.

scholarly journals Modeling Water Resources: Have We Got it Right?

2000 ◽  
Vol 1 ◽  
pp. 5-6
Author(s):  
Karl E. Havens
Keyword(s):  
Decision Making ◽  
Water Resources ◽  
Observational Data ◽  
Scientific Information ◽  
Empirical Models ◽  
Controlled Experiments ◽  
Ecological Processes ◽  
Ecosystem Responses ◽  
Resource Managers ◽  
Complex Ecosystem

Aquatic scientists generally recognize that controlled experiments are required to establish cause-effect relationships (e.g., Havens and Aumen, 2000), and understanding ecological processes is key to accurately predicting complex ecosystem responses. However, resource managers may have at their disposal only a limited amount of observational data when faced with management decisions. Hence, there may be a tendency to use simple empirical models for decision making. An example of eutrophication management in lakes illustrates a pitfall of this approach when used independently of other scientific information.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

Turnover is replaced by nestedness with increasing geographical distance in bacterial communities of coastal shallow lakes

2020 ◽  
Vol 71 (9) ◽  
pp. 1086
Author(s):  
Marla Sonaira Lima ◽  
Fabiana Schneck ◽  
Ng Haig They ◽  
Luciane Oliveira Crossetti ◽  
Juliana Elisa Bohnenberger ◽  
...  
Keyword(s):  
Shallow Lakes ◽  
Bacterial Communities ◽  
Local Environment ◽  
Dispersal Limitation ◽  
Geographical Distance ◽  
Environmental Filters ◽  
Species Sorting ◽  
Relative Contribution ◽  
Β Diversity ◽  
The Relationship

In this study we measured the relative contribution of two components of β-diversity, turnover and nestedness, of bacterioplankton among 25 shallow lakes in southern Brazil and tested their relationship with local (environment, chlorophyll-a and biomass of phytoplanktonic classes) and landscape variables, as well as geographical distance. We predicted that turnover would be the largest share of total β-diversity due to the variation of local characteristics among lakes. Further, we expected nestedness to increase at the expense of turnover with increasing geographical distance among lakes due to dispersal limitation. The results indicated a higher contribution of turnover than nestedness to total β-diversity, which was driven by local factors. When the relationship between β-diversity components and the spatial extent between each lake and all other lakes was considered, turnover was replaced by nestedness with increasing geographical distance for 8 (the furthermost lakes) of the 25 lakes likely because of a combination of decreasing dispersal due to distance and richness differences due to wind-driven mass effects. The results of this study suggest a role for nestedness as an indicator of dispersal limitation owing to geographical distance and wind dispersal, and for turnover as an indicator of species sorting because of environmental filters for these freshwater bacterial communities.

scholarly journals Microbial communities of soda lakes and pans in the Carpathian Basin: a review

2020 ◽  
Vol 71 (4) ◽  
pp. 393-404 ◽  
Author(s):  
Tamás Felföldi
Keyword(s):  
Bacterial Communities ◽  
Current Knowledge ◽  
Soda Lakes ◽  
Grazing Pressure ◽  
Carpathian Basin ◽  
Nutrient Load ◽  
Ecological Processes ◽  
Microbial Groups ◽  
Physical And Chemical ◽  
External Nutrient

AbstractIn this review, I would like to summarize the current knowledge on the microbiology of soda lakes and pans of the Carpathian Basin. First, the characteristic physical and chemical features of these sites are described. Most of the microbiological information presented deals with prokaryotes and algae, but protists and viruses are also mentioned. Planktonic bacterial communities are dominated by members of the phyla Actinobacteria, Bacteroidetes and Proteobacteria; small-sized trebouxiophycean green algae and Synechococcus/Cyanobium picocyanobacteria are the most important components of phytoplankton. Based on the current knowledge, it seems that mainly temperature, salinity, turbidity and grazing pressure regulate community composition and the abundance of individual microbial groups, but the external nutrient load from birds also has a significant impact on the ecological processes.

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