Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Water Research, Год журнала: 2020, Номер 191, С. 116767 - 116767

Опубликована: Дек. 23, 2020

Bioindication has become an indispensable part of water quality monitoring in most countries the world, with presence and abundance bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea protists) are seldom as bioindicators routine assessments, although they have been recognized their importance environmental processes. Recently, use molecular methods revealed unexpected diversity within known functional groups novel metabolic pathways that particularly important energy nutrient cycling. various habitats, microbial communities respond to eutrophication, metals, natural or anthropogenic organic pollutants through changes function. this review, we evaluated common trends these changes, documenting value can be not only but also improving our understanding major processes lotic lentic environments. Current knowledge provides a solid foundation exploiting community structures diversity, well genes, programs. These measures combined into indices, resolution individual bioindicators. Here, assess particular approaches complemented by advanced bioinformatic analysis, promising respect detailed bioindication value. We conclude dynamics missing link rapid structure function aquatic ecosystems, should addressed future freshwater ecosystems.

Язык: Английский

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Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession

Nature Microbiology, Год журнала: 2021, Номер 6(4), С. 479 - 488

Опубликована: Янв. 28, 2021

Язык: Английский

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Dissolved oxygen deficits in a shallow eutrophic aquatic ecosystem (fishpond) – Sediment oxygen demand and water column respiration alternately drive the oxygen regime

The Science of The Total Environment, Год журнала: 2020, Номер 766, С. 142647 - 142647

Опубликована: Окт. 8, 2020

Язык: Английский

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High-resolution metagenomic reconstruction of the freshwater spring bloom

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Янв. 26, 2023

Abstract Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts microbial assemblages during after the have been reported, genomic information on community of remains scarce. Results We performed high-resolution spatio-temporal sampling reservoir describe multitude previously unknown taxa using metagenome-assembled genomes eukaryotes, prokaryotes, viruses combination with broad array methodologies. recovered reveal distributional dynamics for several bacterial groups progressively increasing stratification. Analyses abundances concert CARD-FISH revealed remarkably similar situ doubling time estimates dominant genome-streamlined lineages. Discordance between quantitations cryptophytes arising from sequence data microscopic identification suggested presence hidden, yet extremely abundant aplastidic were confirmed by analyses. Aplastidic are prevalent throughout water column but never considered prior models plankton dynamics. also first metagenomic-assembled protists (a diatom haptophyte) along thousands giant viral contigs, some which appeared to infecting haptophytes owing lack known representatives, most remained without any indication their hosts. contrasting distribution present entire parasitic perkinsids residing largely deeper waters allows us propose as agents top-down control collapse, likely bottom-up factors like nutrient limitation. Conclusion reconstructed microbes show such large-scale genome recovery tracking planktonic succession great detail. However, integration metagenomic other methodologies (e.g., microscopy, CARD-FISH) critical diverse phenomena patterns, times) novel participants cryptophytes) further refine existing affecting collapse). This work provides foundation future approaches towards fine-scale characterization organisms relation rapidly changing environment course bloom.

Язык: Английский

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Factors shaping community patterns of protists and bacteria on a European scale

Environmental Microbiology, Год журнала: 2020, Номер 22(6), С. 2243 - 2260

Опубликована: Март 23, 2020

Summary Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival individual taxa maintenance diversity. In recent years, a contribution geographic distance dispersal barriers to distribution protists bacteria has been demonstrated. Organismic interactions such as competition, predation mutualism further modify structure distinct taxa. Here, we address relative importance these different in bacterial communities on European scale using high‐throughput sequencing data obtained from lentic freshwater ecosystems. We show that similar those bacteria. Our results indicate cross‐domain organismic important variables with higher influence compared Abiotic physical also contributed significantly patterns. The latter was for bacteria, which may reflect stronger biogeochemical coupling. geographical both microbial groups.

Язык: Английский

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CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Frontiers in Microbiology, Год журнала: 2021, Номер 12

Опубликована: Март 4, 2021

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so microbial eukaryotes. Application this technique that Paraphysomonas or Spumella -like chrysophytes, considered among the most prominent members protistan communities pelagic environments, omnipresent actually abundant than expected, contrast little known groups heterotrophic cryptophyte (e.g., CRY1), cercozoans, katablepharids, MAST lineages. Combination with tracer techniques application double allow visualization vacuole contents flagellate groups, thus considerably challenging our current, simplistic view they predominantly bacterivores. Experimental manipulations natural larger flagellates omnivores ingesting both prokaryotes other protists. These new findings justify proposition an updated model webs reflecting more authentically complex trophic interactions roles flagellated protists, inclusion at least two additional levels nanoplankton size fraction. Moreover, we provide a detailed protocol for exemplified mixo- nanoplanktonic flagellates, together tips probe design, troubleshooting guide addressing frequent obstacles, exhaustive list published probes targeting

Язык: Английский

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A dataset on trophic modes of aquatic protists

Biodiversity Data Journal, Год журнала: 2020, Номер 8

Опубликована: Окт. 23, 2020

An important functional trait of organisms is their trophic mode. It determines position within food webs, as well function an ecosystem. For the better part 20th century, aquatic protist communities were thought to consist mainly producers (phytoplankton) and consumers (protozooplankton). Phytoplankton cover energy requirements through photosynthesis (phototrophy), while protozooplankton graze on prey organic particles (phagotrophy). However, over past decades, it was shown that another group (mixoplankton) comprise a notable communities. Mixoplankton employ third mode by combining phototrophy phagotrophy (mixotrophy). Due historical dichotomy, not straightforward gain adequate correct information protists. Long hours literature research or expert knowledge are needed correctly assign modes. Additionally, protists also have long history undergoing taxonomic changes which make difficult compare present literature. While WoRMS, World Register Marine Species, keeps track assigns each species unique AphiaID can be linked its various historic hierarchy, there currently no machine-readable database query for modes.This paper describes dataset submitted WoRMS links taxa, with focus marine The bulk data used this stems from (routine) monitoring stations in North Sea Baltic Sea. augmented checked against state-of-the-art mixoplankton taxa consulting experts. Thus, provides first attempt easily accessible both human- format.

Язык: Английский

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Insight into Unprecedented Diversity of Cyanopeptides in Eutrophic Ponds Using an MS/MS Networking Approach

Toxins, Год журнала: 2020, Номер 12(9), С. 561 - 561

Опубликована: Авг. 31, 2020

Man-made shallow fishponds in the Czech Republic have been facing high eutrophication since 1950s. Anthropogenic and feeding of fish strongly affected physicochemical properties water its aquatic community composition, leading to harmful algal bloom formation. In our current study, we characterized phytoplankton across three eutrophic ponds assess dynamics during vegetation season. We microscopically identified quantified 29 cyanobacterial taxa comprising non-toxigenic toxigenic species. Further, a detailed cyanopeptides (CNPs) profiling was performed using molecular networking analysis liquid chromatography-tandem mass spectrometry (LC-MS/MS) data coupled with dereplication strategy. This MS approach, dereplication, on online global natural product social (GNPS) web platform led us putatively identify forty CNPs: fourteen anabaenopeptins, ten microcystins, five cyanopeptolins, six microginins, two cyanobactins, dipeptide radiosumin, cyclooctapeptide planktocyclin, epidolastatin 12. applied binary logistic regression estimate CNPs producers by correlating GNPS species abundance. The usage proved valuable approach for rapid simultaneous detection large number peptides risk assessments blooms.

Язык: Английский

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Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network

Microorganisms, Год журнала: 2021, Номер 9(3), С. 549 - 549

Опубликована: Март 6, 2021

Network analyses of biological communities allow for identifying potential consequences climate change on the resilience ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed protistan plankton co-occurrence network Lake Zurich, model lake ecosystem subjected change. Despite several documentations dramatic warming in our study provides an unprecedented perspective by linking changes biotic association patterns stress. Water temperature belonged strongest environmental parameters splitting data into two distinct seasonal networks (October–April; May–September). The expected ecological niche phytoplankton, weakened through nutrient depletion because permanent thermal stratification parasitic fungi, was occupied cyanobacterium Planktothrix rubescens mixotrophic nanoflagellates. Instead bacteria nanoflagellates were main prey organisms associated with key predators (ciliates), which contrasts traditional views associations plankton. In species extinction scenario, warm season emerged as more vulnerable than cold network, indicating time-lagged effect warmer winter temperatures communities. We conclude that stressors compromise replacement, richness differences, succession indicated properties.

Язык: Английский

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Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution

Frontiers in Microbiology, Год журнала: 2022, Номер 12

Опубликована: Фев. 4, 2022

Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In pelagial lakes, about 20 urotrich species occur throughout an annual cycle, some which play a pivotal role aquatic food webs. For example, during phytoplankton spring bloom, they consume remarkable proportion algal production. ecological studies, ciliates usually merely identified to rank and grouped into size classes. This is unsatisfying considering distinct autecological properties individual their specific spatial temporal distribution patterns. As basis for future research, we characterized detail four common morphotypes, i.e., specimens as U. furcata tentatively agilis, pseudofurcata, castalia, using state-of-the-art methods. We used integrative polyphasic approach, morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with molecular approach exploiting different gene fragments taxonomic DNA barcodes resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 V9 regions SSU rDNA). shed light on diversity well global patterns, cycles. Additionally, coupled occurrences environmental parameters, subsequently modeled occurrence, logistic regressions. Furthermore, one strain putatively ascertained optimal cultivation media preferences. Thereby, our comprehensive view these important that frequently high throughput sequencing datasets worldwide will allow better exploit protistan data from lakes.

Язык: Английский

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