Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

ABSTRACTDiversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.IMPORTANCEThe diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.

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STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽

10.18860/elha.v1i4.1785 ◽

2012 ◽

Vol 1 (4) ◽

Author(s):

Prihastuti Prihastuti

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Microbial Communities ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Organic Soil ◽

Plant Type ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Wide Range

Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition. Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles. The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions. That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.Keywords: structure, microbial, implication, sustainable agriculture

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Nectar Microbial Diversity and Changes Associated with Environmental Exposure

10.21203/rs.3.rs-46958/v1 ◽

2020 ◽

Author(s):

Claire E Lamb ◽

Caroline L Marden ◽

Alexandra Ebeling ◽

Rocio Perez-Barrales ◽

Joy E.M. Watts

Keyword(s):

Microbial Diversity ◽

Antimicrobial Properties ◽

Fungal Species ◽

Community Diversity ◽

Suitable Habitat ◽

Sequencing Analysis ◽

Floral Nectar ◽

Core Microbiome ◽

Flower Nectar ◽

Wide Range

Abstract Background: Plants are critical to global environmental health and food production strategies; most plants utilise flowers as part of their reproduction cycle. Flowers attract pollinators using a range of complex strategies and floral nectar is an essential component of this attraction profile. Nectar is a nutrient rich liquid, containing a range of sugars, organic acids, amino acids, lipids and vitamins, found to be a suitable habitat for a wide range of fungi, but so far, limited bacterial diversity has been detected. Several antimicrobial properties and adverse environmental conditions, such as high osmotic pressure present in the nectar were thought to reduce bacterial numbers.Results: This study reports the next generation sequencing analysis of the bacterial and fungal diversity in flower nectar. This was achieved in four floral species native to the United Kingdom (Lamium album, white dead nettle; Narcissus pseudonarcissus, daffodil, Hyacinthoides non-scripta, English bluebell and Digitalis purpurea, the common foxglove). All flower species examined had a diverse bacterial and fungal populations present with a core microbiome detected, dominated by Proteobacteria and Firmicutes phyla, while Basidomycota were the most persistent fungal phyla in all of the floral nectar types sampled. However, many unique bacterial and fungal species were detected at lower abundances. Furthermore, in N. pseudonarcissus and D. purpurea floral nectar, the microbial diversity detected in the nectar between flowers exposed to the environment versus non-environment exposed flowers, was different.Conclusions: These results suggest that floral nectars in different plant species do contain a distinct microbiome and the individual flower microbial community diversity may be affected by floral nectar composition, insect visitation and other environmental factors.

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Networks of energetic and metabolic interactions define dynamics in microbial communities

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1506034112 ◽

2015 ◽

Vol 112 (50) ◽

pp. 15450-15455 ◽

Cited By ~ 116

Author(s):

Mallory Embree ◽

Joanne K. Liu ◽

Mahmoud M. Al-Bassam ◽

Karsten Zengler

Keyword(s):

Microbial Communities ◽

Community Diversity ◽

Metagenomic Data ◽

Interspecies Interactions ◽

Environmental Perturbations ◽

Technological Advances ◽

Metabolic Interactions ◽

High Species Richness ◽

Species Specific ◽

And Control

Microorganisms form diverse communities that have a profound impact on the environment and human health. Recent technological advances have enabled elucidation of community diversity at high resolution. Investigation of microbial communities has revealed that they often contain multiple members with complementing and seemingly redundant metabolic capabilities. An understanding of the communal impacts of redundant metabolic capabilities is currently lacking; specifically, it is not known whether metabolic redundancy will foster competition or motivate cooperation. By investigating methanogenic populations, we identified the multidimensional interspecies interactions that define composition and dynamics within syntrophic communities that play a key role in the global carbon cycle. Species-specific genomes were extracted from metagenomic data using differential coverage binning. We used metabolic modeling leveraging metatranscriptomic information to reveal and quantify a complex intertwined system of syntrophic relationships. Our results show that amino acid auxotrophies create additional interdependencies that define community composition and control carbon and energy flux through the system while simultaneously contributing to overall community robustness. Strategic use of antimicrobials further reinforces this intricate interspecies network. Collectively, our study reveals the multidimensional interactions in syntrophic communities that promote high species richness and bolster community stability during environmental perturbations.

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The effect of flue-curing procedure on the dynamic change of microbial diversity of tobaccos

Scientific Reports ◽

10.1038/s41598-021-84875-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Binbin Hu ◽

Kaiyuan Gu ◽

Jiangshiqi Gong ◽

Ke Zhang ◽

Dan Chen ◽

...

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Theoretical Basis ◽

High Throughput Sequencing ◽

Dynamic Change ◽

Community Diversity ◽

Curing Process ◽

Tobacco Leaves ◽

Culture Independent ◽

Curing Procedure

AbstractThe purpose of the study is to explore the effect of flue-curing procedure on the diversity of microbial communities in tobaccos and the dynamic change of compositions of microbial communities in the flue-curing process. It expects to provide a theoretical basis for the application of microbes in tobacco leaves and a theoretical basis and idea for optimization of the flue-curing technologies. By investigating tobacco variety K326, the tests were carried out for comparing the conventional flue-curing procedure and dry-ball temperature set and wet-ball temperature degradation flue-curing procedure. Based on the culture-independent approach and high-throughput sequencing procedure, the relationship between the flue-curing procedure for tobaccos and microbial communities in tobaccos was revealed by measuring the dynamic change of microbial communities. The results indicated that:(1) Relative to surface wiping method, washing method was more suitable for the sampling of microbes on the surface of tobacco leaves; (2) Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure was more favorable for maintaining the microbial diversity of tobaccos; (3) Relative to bacteria of the tobaccos, the succession rule of the fungal communities in tobaccos was relatively steady; (4)Compared with bacterial community diversity, the fungal community diversity presented an obvious negative correlation with temperature and humidity during the flue-curing process. (5) The function of bacterial communities in tobaccos matched with the material transformation law of tobaccos, having a direct correlation on the flue-curing process. In short, Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure can more favorably maintain the microbial diversity of tobaccos; moreover, the function of the tobacco system involved in microbes in tobaccos was closely related to the material transformation law of tobaccos in the flue-curing process. It validated that the bacteria in tobaccos play an important role in the flue-curing process of tobaccos.

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Soil microbial diversity impacts plant microbiomes more than herbivory

10.1101/2020.09.30.320317 ◽

2020 ◽

Author(s):

Antonino Malacrinò ◽

Alison J. Karley ◽

Leonardo Schena ◽

Alison E. Bennett

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Plant Species ◽

Plant Protection ◽

Relative Strength ◽

Community Diversity ◽

Soil Microbiome ◽

Soil Microbial Diversity ◽

Microbiome Composition ◽

Soil Microbial

AbstractInteractions between plants and microbiomes play a key role in ecosystem functioning, and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, for the first time, we show interactions between plant-associated microbial communities that drive their diversity and community composition. We manipulated soil microbial diversity, plant species, and herbivory, and found that soil microbial diversity influenced the herbivore-associated microbiome composition, but also plant species and herbivory influenced the soil microbiome composition. We used a novel approach, quantifying the relative strength of these effects, and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems.

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Soil microbial diversity impacts plant microbiota more than herbivory

Phytobiomes Journal ◽

10.1094/pbiomes-02-21-0011-r ◽

2021 ◽

Author(s):

Antonino Malacrinò ◽

Alison Karley ◽

Leonardo Schena ◽

Alison Bennett

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Plant Species ◽

Plant Protection ◽

Community Diversity ◽

Macrosiphum Euphorbiae ◽

Soil Microbiome ◽

Soil Microbial Diversity ◽

Microbiome Composition ◽

Soil Microbial

Interactions between plants and microbiomes play a key role in ecosystem functioning and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, we tested and quantified the effect of different factors driving the diversity and composition of plant-associated microbial communities. We manipulated soil microbial diversity (high or low diversity), plant species (Solanum tuberosum or Solanum vernei), and herbivory (presence or absence of a phloem-feeding insect Macrosiphum euphorbiae), and found that soil microbial diversity influenced the herbivore-associated microbiome composition, but also plant species and herbivory influenced the soil microbiome composition. We quantified the relative strength of these effects and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems.

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Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics

10.1101/389379 ◽

2018 ◽

Author(s):

Lizbeth Dávila-Santiago ◽

Natasha DeLeón-Rodriguez ◽

Katia LaSanta-Pagán ◽

Janet K. Hatt ◽

Zohre Kurt ◽

...

Keyword(s):

Puerto Rico ◽

Microbial Diversity ◽

Microbial Communities ◽

Natural Attenuation ◽

Anthropogenic Impacts ◽

Military Training ◽

Reference Points ◽

Community Diversity ◽

Metagenomic Sequencing ◽

The Impact

AbstractThe Anones Lagoon, located in the island municipality of Vieques, Puerto Rico (PR), received extensive bombing during military practices by the US Navy for decades. After military activities ceased in 2003, the bombing range was designated as part of a larger Superfund site by US EPA. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR’s capital city). Consistent with selection under low anthropogenic impacts, Guaniquilla exhibited the highest degree of diversity with lower frequency of genes related to xenobiotics metabolism among the three lagoons. Notably, a clear shift was observed in Anones, withEuryarchaeotabecoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique population genomes were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants. Collectively, these results provided new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and could serve as reference points to enhance bioremediation actions at this site and for assessing other similarly impacted sites.ImportanceThis study represents the first assessment of the benthic microbial community in the Anones Lagoon in Vieques, Puerto Rico after the impact of intense pollution by bombs and unconventional weapons during military training exercises. Evaluating the microbial diversity of Anones, represents an opportunity to assess the microbial succession patterns during the active process of natural attenuation of pollutants. The culture-independent techniques employed to study these environmental samples allowed the recovery of almost complete genomes of several abundant species that were likely involved in the biodegradation of pollutants and thus, represented species responding to the strong selection pressure posed by military activities. Further, our results showed that natural attenuation has proceeded to a great extend ten years after the cease of military activities.

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Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

Applied and Environmental Microbiology ◽

10.1128/aem.01459-12 ◽

2012 ◽

Vol 78 (21) ◽

pp. 7527-7537 ◽

Cited By ~ 104

Author(s):

David R. Andrew ◽

Robert R. Fitak ◽

Adrian Munguia-Vega ◽

Adriana Racolta ◽

Vincent G. Martinson ◽

...

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Sonoran Desert ◽

Abiotic Factors ◽

Extreme Environments ◽

Community Diversity ◽

Rrna Gene ◽

Content Type ◽

Bacterial Phyla ◽

Culture Independent

ABSTRACTHigh-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundantCrenarchaeotaclassThermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phylaProteobacteria,Actinobacteria,Planctomycetes,Firmicutes,Bacteroidetes,Chloroflexi, andAcidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

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A simple linear relationship between resource availability and microbial community diversity

10.1101/2020.09.12.294660 ◽

2020 ◽

Author(s):

Martina Dal Bello ◽

Hyunseok Lee ◽

Akshit Goyal ◽

Jeff Gore

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Linear Relationship ◽

Resource Availability ◽

Carbon Sources ◽

Community Diversity ◽

Microbial Community Diversity ◽

Wide Range ◽

Simple Linear Relationship

AbstractMicrobial community diversity is pivotal for the functioning of our planet, but its drivers are still unclear, in particular the role of resource number and identity. To fill this gap, we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found a remarkable diversity in single resources but a linear one-by-one increase in the number of species with the number of additional resources. We show, both experimentally and theoretically, that both these observations could originate from generalist and specialist taxa interacting in a modular fashion within the community. Since generalists and specialists are ubiquitous in natural microbiomes, our results might apply to a variety of different ecological settings, providing a framework to predict how community diversity responds to changes in resource availability.One Sentence SummaryWhile many species coexist in single resources, community diversity only increases one-by-one as more resources are added.

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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