Spatial diversity of planktonic protists in the Lagoon of Venice (LTER-Italy) based on 18S rDNA

Transitional waters are subject to a high degree of variability in space and time. In this study, protist plankton communities of the Lagoon of Venice were compared among four sites characterised by different environmental conditions with a metabarcoding approach. High throughput sequencing (HTS) of the V4-18S rDNA fragment in 32 samples collected on four dates, from April 2016 to February 2017, produced 1,137,113 reads, which were grouped into 4,058 OTUs at 97% similarity. Bacillariophyta and Ciliophora were the most abundant groups in the entire dataset in terms of read number (27.6% and 16.6%, respectively), followed by Dinophyta (10.9%), Cryptophyceae (9.7%), and Syndiniales (6.1%). The contribution of protist groups markedly varied across the seasons, but spatial differences were also recorded in the lagoon. In April, a higher contribution of Bacillariophyta characterized St1 and 5 (68.0% and 61.1%), whereas Sts2 and 3 showed a higher percentage of Ciliophora (18.6 and 23.4%, respectively) and dinoflagellates (10.3 and 7.7%). In July, diatom blooms occurred at Sts1, 2 and 3, with some differences in the dominant species. At St2 Dinophyta reached the highest contribution of the whole sampling period in the area (30.6%), while St5 was quite distinct, with a low contribution of diatoms and a dominance of Ciliophora (34.0%) and Trebouxiophyceae (36.4%). All the stations in November were characterized by relatively high abundance of Ciliophora (21.4-51.9%). In February, diatom contribution was relevant only at St5 (29.3%), Teleaulax acuta peaked at St3 (ca. 36%), Syndiniales at St2 (38.8%) and Dictyochophyceae at St1 (24.2%). The α-diversity indexes (observed OTUs, Shannon and Pielou evenness) showed a high variability over space and time. Overall, diversity and community composition were rather similar between the intermediate and deeper Sts2 and 3 on all sampling dates whereas they at time differed between the landward and shallow Sts1 and 5. While the most marked differences occurred over the temporal scale, the depth of the station and the relatedness with the external marine coastal environment appear to play a major role in the spatial distribution of protist communities within the lagoon.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa195 ◽

2020 ◽

Vol 96 (12) ◽

Author(s):

Hang Qian ◽

Chunli Hou ◽

Hao Liao ◽

Li Wang ◽

Shun Han ◽

...

Keyword(s):

Soil Properties ◽

Paddy Soil ◽

High Throughput Sequencing ◽

Abiotic Factors ◽

Negative Relationship ◽

Sequencing Analysis ◽

Nitrogen Use ◽

Microbial Network ◽

Α Diversity ◽

Positive Effect

ABSTRACT To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.

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Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Applied and Environmental Microbiology ◽

10.1128/aem.00560-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4757-4766 ◽

Cited By ~ 55

Author(s):

Caterina R. Giner ◽

Irene Forn ◽

Sarah Romac ◽

Ramiro Logares ◽

Colomban de Vargas ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput ◽

Relative Abundance ◽

Ribosomal Dna ◽

18S Rdna ◽

High Throughput Sequencing ◽

454 Sequencing ◽

Epifluorescence Microscopy ◽

Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽

10.3390/antibiotics7020027 ◽

2018 ◽

Vol 7 (2) ◽

pp. 27 ◽

Cited By ~ 8

Author(s):

Marta Maciejewska ◽

Magdalena Całusińska ◽

Luc Cornet ◽

Delphine Adam ◽

Igor Pessi ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Spatial Diversity ◽

Sequencing Analysis

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The Influence of Food Intake Specificity in Children with Autism on Gut Microbiota

International Journal of Molecular Sciences ◽

10.3390/ijms21082797 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2797 ◽

Cited By ~ 4

Author(s):

Aleksandra Tomova ◽

Katarina Soltys ◽

Petra Kemenyova ◽

Miloslav Karhanek ◽

Katarina Babinska

Keyword(s):

Gut Microbiota ◽

Food Habits ◽

High Throughput Sequencing ◽

Fermented Milk ◽

Autism Spectrum ◽

Food Selectivity ◽

Omega 3 ◽

Fibre Intake ◽

Children With Asd ◽

Α Diversity

Autism spectrum disorder (ASD) is a complex of neurodevelopmental conditions with increasing incidence. The microbiota of children with ASD is distinct from neurotypical children, their food habits are also different, and it is known that nutrient intake influences microbiota in a specific way. Thus, this study investigates the food habits of children with ASD and their association with the gut microbiota. Children with ASD had their dietary energy intakes similar to controls, but they more often demonstrated food selectivity, which seemed to result in deficiency of micronutrients such as vitamins K, B6, C, iron, cooper, docosahexaenoic and docosapentanoic acid. Using high-throughput sequencing, a DNA library of intestinal microbiota was performed. Core microbiota was similar in children with and without ASD, but Dichelobacter, Nitriliruptor and Constrictibacter were found to be putative markers of ASD. The changes in gut microbiota that we observed in connection to food selectivity, intake of fats and omega-3 in particular, fermented milk products and animal/plant protein consumption had similar character, independent of diagnosis. However, high fibre intake was connected with a decreased α-diversity only in children with ASD. High carbohydrate and fibre intake influenced β-diversity, changing the abundance of Bacteroides and other genera, many of them members of the Clostidiaceae. Modulating food habits of ASD children can influence their gut microbiota composition.

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Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

Applied and Environmental Microbiology ◽

10.1128/aem.02885-17 ◽

2018 ◽

Vol 84 (9) ◽

Cited By ~ 15

Author(s):

Bing Li ◽

Wei-Min Wu ◽

David B. Watson ◽

Erick Cardenas ◽

Yuanqing Chao ◽

...

Keyword(s):

Network Analysis ◽

High Throughput ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Ecological Niches ◽

Content Type ◽

Oak Ridge ◽

Α Diversity ◽

Before And After

ABSTRACTA site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilizedin situthrough intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A pairedttest indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion.Castellaniellahad the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing generaGeothrix,Desulfovibrio,Ferribacterium, andGeobacterdecreased significantly, whereas the denitrifyingAcidovoraxabundance increased significantly after groundwater invasion. Additionally, seven genera, i.e.,Castellaniella,Ignavibacterium,Simplicispira,Rhizomicrobium,AcidobacteriaGp1,AcidobacteriaGp14, andAcidobacteriaGp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCEHigh-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

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An evaluation of the accuracy and speed of metagenome analysis tools

Scientific Reports ◽

10.1038/srep19233 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 187

Author(s):

Stinus Lindgreen ◽

Karen L. Adair ◽

Paul P. Gardner

Keyword(s):

Aquatic Ecosystems ◽

Large Scale ◽

High Throughput Sequencing ◽

Data Sets ◽

Metagenome Analysis ◽

Analysis Tools ◽

Sequencing Platforms ◽

Capacity Data ◽

High Degree ◽

Realistic Data

Abstract Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html

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Ground-truthing Phylotype Assignments for Antarctic Invertebrates

DNA Barcodes ◽

10.1515/dna-2017-0001 ◽

2017 ◽

Vol 5 (1) ◽

pp. 1-13

Author(s):

Paul Czechowski ◽

Laurence Clarke ◽

Alan Cooper ◽

Mark Stevens

Keyword(s):

18S Rdna ◽

High Throughput Sequencing ◽

Antarctic Soils ◽

Reference Information ◽

Artificial Dna ◽

Terrestrial Habitats ◽

Ground Truthing ◽

Taxonomic Assignments ◽

Taxonomic Groups ◽

Biodiversity Information

AbstractBiodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, hence DNA-based metabarcoding methods are well suited for their study. We compared taxonomy assignments of a high throughput sequencing metabarcoding approach using one ribosomal DNA (18S rDNA) and one mitochondrial DNA (cytochrome c oxidase subunit I - COI) marker with morphological reference data. Specifically, we compared metabarcoding or morphological taxonomic assignments on multiple taxonomic levels in an artificial DNA blend containing Australian invertebrates, and in seven extracts of Antarctic soils containing known micro-faunal taxa. Avoiding arbitrary application of metabarcoding analysis parameters, we calibrated those parameters with metabarcoding data from non-Antarctic soils. Metabarcoding approaches employing 18S rDNA and COI markers enabled detection of small and cryptic Antarctic invertebrates, and on low taxonomic ranks 18S data outperformed COI data in this respect. Morphological taxonomy determination did not outperform metabarcoding approaches. Our study demonstrates how barcoding markers can be tested prior to their application to specific taxonomic groups, and that taxonomy fidelity of markers needs to be validated in relation to environment, taxa, and available reference information.

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Temporal pattern prevails over spatial variability in phytoplankton communities from a subtropical water supply reservoir

Oceanological and Hydrobiological Studies ◽

10.2478/s13545-013-0098-3 ◽

2013 ◽

Vol 42 (4) ◽

Cited By ~ 9

Author(s):

Hong Lv ◽

Jun Yang ◽

Lemian Liu

Keyword(s):

Sampling Period ◽

Wiener Index ◽

Ammonium Nitrogen ◽

Cylindrospermopsis Raciborskii ◽

Spatial Factor ◽

Phytoplankton Communities ◽

Spatial Differences ◽

Deep Reservoir ◽

Term Monitoring

AbstractPhytoplankton species are dominant components in reservoir ecosystems, yet little is known about their variability and dynamics, especially along the depth continuum. This study examined vertical and horizontal differences in phytoplankton communities in a typical subtropical deep reservoir (i.e. Dongzhen Reservoir) from 2011 to 2012. Phytoplankton communities separated into four groups based on the biomass data, indicating that temporal differences in the community structure were greater than spatial differences. Autumn communities had the highest diversity measured by the Shannon-Wiener index (2.47±0.07), while summer communities had the lowest diversity (0.46±0.09). Both winter and spring communities were dominated by diatoms (90.4±1.7%), while cyanobacteria dominated in summer communities during our sampling period. In spring and summer, however, the three surface communities characterized by high biomass were most similar to each other, indicating that vertical variation was significantly higher than horizontal differences. Furthermore, Cylindrospermopsis raciborskii accounted for over 96% of the total phytoplankton biomass in the summer surface water. The redundancy analysis (RDA) illustrated that the temporal factor (summer), the spatial factor (depth), and nutrients (nitrite and nitrate nitrogen, ammonium nitrogen, phosphate phosphorus) were significant variables affecting the dynamics of phytoplankton communities. High temperature with stable thermal stratification might have been the cause of C. raciborskii dominance in Dongzhen Reservoir in summer. Regular and long-term monitoring of dominant species is urgently needed for water quality protection and sustainable reservoir management. Copyright© of Dept. of Oceanography and Geography, University of Gdańsk, Poland

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Waste from the agricultural sector in the European Union countries in the context of the bioeconomy development

Agronomy Science ◽

10.24326/as.2019.4.3 ◽

2020 ◽

Vol 74 (4) ◽

pp. 47-59

Author(s):

AGNIESZKA KOMOR ◽

BARBARA BUJANOWICZ-HARAŚ

Keyword(s):

The Netherlands ◽

Agricultural Sector ◽

Spatial Diversity ◽

Research Area ◽

Animal Waste ◽

The European Union ◽

High Position ◽

Eu Countries ◽

High Degree ◽

The Eu

The aim of the study was to identify and assess the spatial diversity of generating of animal and vegetal waste by entities from the agricultural sector in the EU countries along with the determination of the importance of this type of waste in total waste generated in individual countries. Statistical data used in the study were obtained from EUROSTAT. The research period was 2016, while the research area covered 25 EU countries. The data was subjected to quantitative analysis using descriptive and parametric statistics. It was found that animal and vegetal waste has the largest share in the structure of waste from the agricultural sector (accounting for 81.6% of all waste in the agricultural sector in the EU in 2016). It has been shown that generating of vegetal and animal waste in agricultural sector in the EU countries is characterized by spatial diversity. Most of this waste type was generated in Spain and the Netherlands. The dominant position of Spain resulted from significant share of this country in the EU volume of animal faeces, urine and manure generation. High position of the Netherlands was associated with a large share of vegetal waste. France, Germany, Slovakia and Sweden ranked next. Nearly 80% of all analyzed groups of waste came from these countries, which indicates a high degree of spatial concentration of the studied phenomenon. In this context, it can be stated that these countries are predestined to base their development on the concept of the bioeconomy. It is a challenge for the research and development sphere regarding development of innovative ways of managing agricultural vegetal and animal waste.

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