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

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.

scholarly journals Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Verónica Lloréns-Rico ◽  
Sara Vieira-Silva ◽  
Pedro J. Gonçalves ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Microbial Communities ◽  
Quantitative Methods ◽  
Microbial Load ◽  
Metagenomic Sequencing ◽  
Sampling Depth ◽  
Microbiome Research ◽  
Microbiome Data ◽  
The Impact ◽  
Analytical Approaches ◽  
Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

Interactions between zebra mussels (Dreissena polymorpha) and microbial communities

2000 ◽  
Vol 57 (3) ◽  
pp. 591-599 ◽  
Author(s):  
Marc E Frischer ◽  
Sandra A Nierzwicki-Bauer ◽  
Robert H Parsons ◽  
Kanda Vathanodorn ◽  
Kelli R Waitkus
Keyword(s):  
Microbial Communities ◽  
Zebra Mussel ◽  
Dreissena Polymorpha ◽  
Hudson River ◽  
Zebra Mussels ◽  
Community Diversity ◽  
Ecological Effect ◽  
Clearance Rates ◽  
Surrounding Water ◽  
The Impact

Zebra mussels (Dreissena polymorpha) have had an enormous impact on aquatic environments. However, little is known concerning their interactions with microbial communities. In these studies, the ability of zebra mussels to derive nutrition from bacterioplankton and their effect on microbial community diversity were investigated in samples from the Hudson River, New York, and in laboratory studies. Clear physiological responses to starvation were observed, including decreases in respiration rates, lipid content, and total weight, that were reversed after feeding zebra mussels a diet of bacteria. Clearance rates of bacteria were correlated with bacteria size (r2= 0.995), with the lowest clearance rates associated with small indigenous river bacteria (size = 0.03 ± 0.04 µm3, clearance rate = 0.08 ± 0.02 mL·mussel-1·min-1). Comparison of the diversity of microbial communities in zebra mussel tissue extract, detritus, and pseudofecal material associated with zebra mussel colonies, surrounding water, and sediment samples revealed distinct microbial assemblages associated with these environments. The overall ecological effect and importance of bacteria - zebra mussel interactions remains unclear, but these studies indicate that these interactions occur and should be included in our efforts to better understand the impact of zebra mussels on aquatic systems.

scholarly journals Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

2019 ◽  
Author(s):  
Emilie Lejal ◽  
Agustín Estrada-Peña ◽  
Maud Marsot ◽  
Jean-François Cosson ◽  
Olivier Rué ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Community Diversity ◽  
Analytical Process ◽  
Sequencing Technologies ◽  
And Gender ◽  
The Impact

AbstractBackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.ResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.ConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

scholarly journals Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Sean M. Gibbons ◽  
Monika Scholz ◽  
Alan L. Hutchison ◽  
Aaron R. Dinner ◽  
Jack A. Gilbert ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Empirical Support ◽  
Community Diversity ◽  
Ecological Communities ◽  
Disturbance Regimes ◽  
Environmental Perturbations ◽  
Compositional Stability ◽  
Wide Range ◽  
Life History Tradeoffs

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.

scholarly journals Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

2020 ◽  
Vol 21 (6) ◽  
pp. 1001-1010 ◽  
Author(s):  
Kathrin Busch ◽  
Lindsay Beazley ◽  
Ellen Kenchington ◽  
Frederick Whoriskey ◽  
Beate M. Slaby ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Anthropogenic Activities ◽  
Amplicon Sequencing ◽  
Habitat Destruction ◽  
Artificial Substrates ◽  
Rrna Gene ◽  
Anthropogenic Pressures ◽  
Glass Sponge

Abstract Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from protected sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in the four sponges from this site and the environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

scholarly journals Erosion reduces soil microbial diversity, network complexity and multifunctionality

2021 ◽  
Author(s):  
Liping Qiu ◽  
Qian Zhang ◽  
Hansong Zhu ◽  
Peter B. Reich ◽  
Samiran Banerjee ◽  
...  
Keyword(s):  
Soil Erosion ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Negative Impact ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Relative Abundances ◽  
The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

scholarly journals Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

2020 ◽  
Author(s):  
Kathrin Busch ◽  
Lindsay Beazley ◽  
Ellen Kenchington ◽  
Frederick Whoriskey ◽  
Beate Slaby ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Anthropogenic Activities ◽  
Amplicon Sequencing ◽  
Habitat Destruction ◽  
Artificial Substrates ◽  
Rrna Gene ◽  
Anthropogenic Pressures ◽  
Glass Sponge

ABSTRACTEstablishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from pristine sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in sponges and environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

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

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.

scholarly journals Land conversion changes soil microbial community structure and diversity

2020 ◽  
Author(s):  
Tong Zhang ◽  
Yufei Liu ◽  
Xin Sui ◽  
Fuqiang Song
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Community Diversity ◽  
Forest Land ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Significant Difference ◽  
The Impact

Abstract Background: To study the impact of land-use change on soil microbial community structure and diversity in Northeast China, three typical land-use types (plough, grassland, and forest), from grassland change to forest land and grassland change to plough, in the Qiqihar region of Heilongjiang Province were taken as research objects. Methods: MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA was used to study the above community structure of soil bacteria and fungi and to explore the relationship between soil bacteria and soil environmental factors. Results: The results showed that there was no significant difference in soil bacterial community diversity and fungal community diversity after the grassland was completely changed to forest land. The dominant bacterial phylum changed from Actinobacteria to Acidobacteria, the dominant fungal phylum changed from Ascomycetes to Basidiomycetes, and the ECM functional group increased significantly. After the grassland was changed to plough, there was no significant difference in the diversity of soil bacterial communities, and the diversity of fungal communities increased significantly. The dominant phylum changed from Actinomycetes to Proteobacteria. The dominant phylum was still Ascomycetes, and the functional groups of pathogens and parasites increased significantly. CCA showed that soil pH, MC, NO3--N, TP and AP were important factors affecting the composition of soil microbial communities, and changes in land-use patterns changed the physical and chemical properties of soils, thereby affecting the structure and diversity of microbial communities. Conclusions: Our research results clarify the impact of changes in land use on the characteristics of soil microbial communities and provide basic data on the healthy use of land.

scholarly journals Soil microbial diversity impacts plant microbiomes more than herbivory

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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