Multiple-Facet Diversity Patterns of Aquatic Vegetation in Lakes along a Trophic Gradient

The EU Water Framework Directive foresees the ecological assessment of surface waters against identified pressures. Nutrient loading is the main pressure impairing the ecological quality of lake ecosystems, and aquatic macrophytes are considered good indicators of ecological response. In this study, we statistically assessed different aspects of aquatic plant (macrophyte) diversity in response to different trophic levels in Mediterranean lakes. We used 5690 relevés of aquatic vegetation, distributed over 305 transects, sampled in 18 freshwater lake ecosystems during 2013–2016. Our results show a significant decrease in taxonomic alpha diversity in lakes with a total phosphorus content above 100 μg/L. Syntaxonomic diversity followed the species richness pattern as well. Functional richness decreased along the trophic gradient, while functional dispersion was higher in lakes with high trophic levels. Taxonomic and functional beta partitioning presented changes in assembly processes leading to greater community homogeneity in lakes with higher trophic levels. In summary, we found no redundancy between taxonomic and functional diversity indices. These results provide novel insights into aquatic plant assembly processes of impacted freshwater lakes needed to forward conservation and restoration practices.

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A phytosociological survey of aquatic vegetation in the main freshwater lakes of Greece

Vegetation Classification and Survey ◽

10.3897/vcs/2020/48377 ◽

2020 ◽

Vol 1 ◽

pp. 53-75

Author(s):

Dimitrios Zervas ◽

Ioannis Tsiripidis ◽

Erwin Bergmeier ◽

Vasiliki Tsiaoussi

Keyword(s):

Plant Communities ◽

Aquatic Plant ◽

Aquatic Vegetation ◽

Environmental Parameters ◽

Hierarchical Cluster ◽

Freshwater Lake ◽

Vegetation Types ◽

Freshwater Lakes ◽

Lake Ecosystems ◽

The Relationship

Aims: This study aims to contribute to the knowledge of European freshwater lake ecosystems with updated and new information on aquatic plant communities, by conducting national-scale phytosociological research of freshwater lake vegetation in Greece. Moreover, it investigates the relationship between aquatic plant communities and lake environmental parameters, including eutrophication levels and hydro-morphological conditions. Study area: Lakes in Greece, SE Europe. Methods: 5,690 phytosociological relevés of aquatic vegetation were sampled in 18 freshwater lake ecosystems during 2013–2016. The relevés were subjected to hierarchical cluster and indicator species analyses in order to identify associations and communities of aquatic vegetation, as well as to describe their syntaxonomy. Multiple regression analysis was applied to investigate the relationship between vegetation syntaxa and environmental parameters of lakes, i.e. physico-chemical parameters and water level fluctuation. Results: Ninety-nine plant taxa belonging to 30 different families were recorded. Forty-six vegetation types were identified and described by their ecological characteristics, diagnostic taxa and syntaxonomical status. Thirteen vegetation types, the largest number belonging to the vegetation class Charetea, are considered to be new records for Greece. The distribution of the vegetation types recorded in the 18 freshwater lakes was found to depend on environmental parameters and levels of eutrophication. Conclusions: An updated aquatic vegetation inventory was produced for Greek lakes, and primary results showed that the presence/absence of aquatic plant communities and the community composition in freshwater lakes can be utilized to assess the pressure of eutrophication on lake ecosystems. Taxonomic reference: Euro+Med (2006–). Abbreviations: MNT = Mean number of taxa; WFD = Water Framework Directive.

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Environmental determinism of community structure across trophic levels: moth assemblages and substrate type in the rain forests of south-western China

Journal of Tropical Ecology ◽

10.1017/s026646741400056x ◽

2014 ◽

Vol 31 (1) ◽

pp. 81-89 ◽

Cited By ~ 2

Author(s):

R. L. Kitching ◽

A. Nakamura ◽

M. Yasuda ◽

A. C. Hughes ◽

Cao Min

Keyword(s):

Soil Type ◽

Alpha Diversity ◽

Diversity Indices ◽

Assemblage Structure ◽

Trophic Levels ◽

Western China ◽

Composition Analysis ◽

Forest Fragments ◽

Dominant Group ◽

Plant Assemblage

Abstract:Soil type may drive vegetation structure. In turn, the richness, identity and diversity of arthropod herbivores may be related to plant diversity through specific host plant relationships in a location. We test the hypothesis that the soil type (calcicolous vs alluvial soils) will drive the assemblage structure of a dominant group of arthropod herbivores: the moths. We used sampling sites in rain-forest fragments in south-western China around the Xishuangbanna Tropical Botanical Gardens (21°41′N, 101°25′E) to test this hypothesis. We used Pennsylvania style light traps to take point samples of macromoths and pyraloids from four sampling sites in forest remnants on a limestone geological base and four from alluvial-based forest. A total of 3165 moths (1739 from limestone-based and 1255 from alluvium-based forests) was collected representing 1255 species. The limestone-based sites showed statistically similar levels of species richness and other alpha diversity indices to the four alluvium-based site. Nevertheless the sites were clearly significantly different in terms of species composition. Analysis of contrasting similarity (‘beta’ diversity) indices suggested that there was ‘leakage’ between the two classes of sites when ‘rare’ species were emphasized in the calculations. We used an indicator value procedure to select species that most characterized this separation. We expect that these differences reflect associated changes in plant assemblage structure acting through the herbivorous habits of larval moths. Accordingly, in any assessment of landscape level diversity the nature of the substrate and its associated vegetation is clearly of great importance. This observation also has consequences for the design of conservation programmes.

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Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

Scientific Reports ◽

10.1038/s41598-021-81507-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hua Zha ◽

Fengping Liu ◽

Zongxin Ling ◽

Kevin Chang ◽

Jiezuan Yang ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Diversity Indices ◽

Vital Role ◽

Rrna Gene ◽

Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

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Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components

Journal of Personalized Medicine ◽

10.3390/jpm11010035 ◽

2021 ◽

Vol 11 (1) ◽

pp. 35

Author(s):

Zahra A. Barandouzi ◽

Joochul Lee ◽

Kendra Maas ◽

Angela R. Starkweather ◽

Xiaomei S. Cong

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Alpha Diversity ◽

Diversity Indices ◽

Cross Sectional Study ◽

Caffeine Intake ◽

Caffeine Consumption ◽

Cross Sectional ◽

Food Components ◽

Irritable Bowel

The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.

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Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota

International Journal of Molecular Sciences ◽

10.3390/ijms22042131 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2131

Author(s):

Stefania Pane ◽

Anna Sacco ◽

Andrea Iorio ◽

Lorenza Romani ◽

Lorenza Putignani

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Alpha Diversity ◽

Strongyloides Stercoralis ◽

Pulmonary Involvement ◽

Diversity Indices ◽

Parasite Infection ◽

Intestinal Nematode ◽

Immune Mediated ◽

Stool Samples

Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples’ ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.

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Reducing Nutrient Loading from Agriculture to Lake Ecosystems – Contributions of Resilience Principles

Water Resilience ◽

10.1007/978-3-030-48110-0_5 ◽

2020 ◽

pp. 91-111

Author(s):

Kate H. Reilly ◽

Elena M. Bennett ◽

Jan F. Adamowski ◽

Gordon M. Hickey

Keyword(s):

Nutrient Loading ◽

Lake Ecosystems

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Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽

10.3390/v13102093 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2093

Author(s):

Shen-Yuan Hsieh ◽

Mohammad A. Tariq ◽

Andrea Telatin ◽

Rebecca Ansorge ◽

Evelien M. Adriaenssens ◽

...

Keyword(s):

Alpha Diversity ◽

Diversity Indices ◽

P Value ◽

Library Preparation ◽

High Genetic Diversity ◽

Sequencing Platform ◽

Viral Genomes ◽

Healthy Donors ◽

Faecal Samples ◽

Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

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Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

Microorganisms ◽

10.3390/microorganisms9112339 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2339

Author(s):

Aleksei O. Zverev ◽

Arina A. Kichko ◽

Aleksandr G. Pinaev ◽

Nikolay A. Provorov ◽

Evgeny E. Andronov

Keyword(s):

Microbial Communities ◽

Plant Communities ◽

Plant Diversity ◽

Beta Diversity ◽

Mutual Influence ◽

Plant Root ◽

Alpha Diversity ◽

Diversity Indices ◽

Alpha And Beta Diversity ◽

Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

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Abundance, diversity and distribution of macrophyte communities in neighboring lakes of different trophic states and morphology in north-central Greece

Archives of Biological Sciences ◽

10.2298/abs1103763p ◽

2011 ◽

Vol 63 (3) ◽

pp. 763-774 ◽

Cited By ~ 2

Author(s):

Chrisoula Pirini ◽

Vasiliki Karagiannakidou ◽

Savvas Charitonidis

Keyword(s):

Environmental Factors ◽

Aquatic Vegetation ◽

Floristic Composition ◽

Diversity Indices ◽

North Central ◽

Wetland Ecosystems ◽

Central Greece ◽

Clear Differentiation ◽

Evenness Indices

The role of aquatic vegetation in wetland ecosystems is closely related with their abundance, diversity and distribution, which in turn represents synergy of various environmental factors. The floristic composition of the aquatic vegetation in two neighboring lakes (Vegoritida and Petron) in north-central Greece was investigated by means of 160 relev?s, which were recorded using the Braun-Blanquet method. The analysis of relev?s based on TWINSPAN clustering showed the existence of 10 plant communities from the Lemnetea, Potametea, Phragmito-Magnocaricetea and Juncetea maritimi classes. The most important environmental factors for the vegetation differentiation in the study area, according to the ordination diagram, are light intensity and water depth of the habitats. The plant species diversity was quantified with species richness, Shannon Diversity and evenness indices at a scale of each relev?, with a sampling size of 20 m2. There was a clear differentiation between the relev?s at the more eutrophic Petron Lake and those at Vegoritida Lake. The mean plot diversity was also calculated for each plant community, to enable comparison of the diversity indices among the communities at the plot level.

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Comparison of different conditions for DNA extraction in sputum - a pilot study

Multidisciplinary Respiratory Medicine ◽

10.4081/mrm.2019.4 ◽

2019 ◽

Vol 14 ◽

Author(s):

Martina Oriano ◽

Leonardo Terranova ◽

Antonio Teri ◽

Samantha Sottotetti ◽

Luca Ruggiero ◽

...

Keyword(s):

Real Time ◽

16S Rdna ◽

Dna Extraction ◽

Real Time Pcr ◽

Alpha Diversity ◽

Diversity Indices ◽

Extraction Yield ◽

Chronic Respiratory Diseases ◽

Dna Yield ◽

Selection Of

Background: The analysis of microbiome in respiratory samples is a topic of great interest in chronic respiratory diseases. The method used to prepare sputum samples for microbiome analysis is very heterogeneous. The selection of the most suitable methodology for DNA extraction is fundamental to have the most representative data. The objective of this study was to compare different conditions for DNA extraction from sputum in adult patients with bronchiectasis. Methods: Five sputum samples from bronchiectasis patients were collected at the Policlinico Hospital in Milan, Italy. Eighteen conditions for DNA extraction were compared, including two enzyme-based (Roche and Zymo) and one beads-based (Mobio) technique. These techniques were tested with/without Dithiothreitol (DTT) and with/without lysostaphin (0.18 and 0.36 mg/mL) step. DNA was quantified, tested using Real-time PCR for 16S rDNA and S. aureus and, then, microbiome was evaluated. Results: Although 16S rDNA was similarly detected across all the different techniques, Roche kit gave the highest DNA yield. The lowest Ct values for Real-time PCR for S. aureus was identified when lysostaphin was added. Considering genera from microbiome, alpha diversity indices did not show any significant differences between techniques, while relative abundances were more similar in presence of DTT. Conclusions: None of the conditions emerged to be superior to the others even if enzyme-based kits seem to be needed in order to have a higher extraction yield.

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