Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

ABSTRACTPhotosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.

Download Full-text

Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz038 ◽

2019 ◽

Vol 95 (5) ◽

Cited By ~ 3

Author(s):

Sebastián Metz ◽

Adriana Lopes dos Santos ◽

Manuel Castro Berman ◽

Estelle Bigeard ◽

Magdalena Licursi ◽

...

Keyword(s):

Flow Cytometry ◽

High Throughput ◽

Shallow Lakes ◽

Cell Sorting ◽

High Throughput Sequencing ◽

Eutrophic Shallow Lakes

Download Full-text

SPATIAL VARIABILITY OF SEDIMENT PHOSPHORUS FRACTIONS IN EUTROPHIC SHALLOW LAKES

10.1130/abs/2018nc-312349 ◽

2018 ◽

Author(s):

Grace Wilkinson ◽

◽

Ellen Albright ◽

Rachel Fleck

Keyword(s):

Spatial Variability ◽

Shallow Lakes ◽

Phosphorus Fractions ◽

Sediment Phosphorus ◽

Eutrophic Shallow Lakes

Download Full-text

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.

Download Full-text

Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

Download Full-text

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

Antarctic Science ◽

10.1017/s0954102021000274 ◽

2021 ◽

pp. 1-10

Author(s):

Micheline Carvalho-Silva ◽

Luiz Henrique Rosa ◽

Otávio H.B. Pinto ◽

Thamar Holanda Da Silva ◽

Diego Knop Henriques ◽

...

Keyword(s):

High Throughput Sequencing ◽

Crater Lake ◽

Environmental Dna ◽

Food Sources ◽

South Shetland Islands ◽

Deception Island ◽

Shetland Islands ◽

Operational Taxonomic Units ◽

First Time ◽

Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

Download Full-text

Relationship between Bacterial Community Composition and Bottom-Up versus Top-Down Variables in Four Eutrophic Shallow Lakes

Applied and Environmental Microbiology ◽

10.1128/aem.68.10.4740-4750.2002 ◽

2002 ◽

Vol 68 (10) ◽

pp. 4740-4750 ◽

Cited By ~ 104

Author(s):

Koenraad Muylaert ◽

Katleen Van der Gucht ◽

Nele Vloemans ◽

Luc De Meester ◽

Moniek Gillis ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Shallow Lakes ◽

Bacterial Community Composition ◽

Top Down ◽

Bottom Up ◽

Rdna Genes ◽

Explanatory Variables ◽

High Nutrient ◽

Eutrophic Shallow Lakes

ABSTRACT Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 μg liter−1) while the other lakes had relatively low nutrient levels (total phosphorus, <100 μg liter−1). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (Daphnia and Ceriodaphnia) was significantly related to changes in the bacterial community in the clearwater lakes. Our results suggest that in eutrophic shallow lakes, seasonality of bacterial community structure is dependent on the dominant substrate source as well as on the food web structure.

Download Full-text

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽

10.3897/mycokeys.39.28109 ◽

2018 ◽

Vol 39 ◽

pp. 29-40 ◽

Cited By ~ 21

Author(s):

Sten Anslan ◽

R. Henrik Nilsson ◽

Christian Wurzbacher ◽

Petr Baldrian ◽

Leho Tedersoo ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Computation Time ◽

Potential Effect ◽

Data Sets ◽

Sequencing Data ◽

Operational Taxonomic Units ◽

High Throughput Sequencing Data ◽

Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

Download Full-text

Molecular diversity of bacteria in commercially available “Spirulina” food supplements

PeerJ ◽

10.7717/peerj.1610 ◽

2016 ◽

Vol 4 ◽

pp. e1610 ◽

Cited By ~ 9

Author(s):

Elisabeth Vardaka ◽

Konstantinos A. Kormas ◽

Matina Katsiapi ◽

Savvas Genitsaris ◽

Maria Moustaka-Gouni

Keyword(s):

Natural Product ◽

454 Pyrosequencing ◽

Molecular Diversity ◽

Arthrospira Platensis ◽

Food Supplements ◽

Health Issues ◽

Operational Taxonomic Units ◽

Health Promoting ◽

First Time ◽

Pyrosequencing Analysis

The cyanobacteriumArthrospirais among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) ofArthrospira platensiswere the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e.,Pseudomonas,Flavobacterium,Vibrio,Aeromonas,Clostridium,Bacillus,Fusobacterium,Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing ofArthrospirabiomass for commercial purposes.

Download Full-text