Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan

Mukherjee, Indranil; Hodoki, Yoshikuni; Nakano, Susumu

doi:10.3354/ame01843

Cited by 16 publications

(26 citation statements)

References 90 publications

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“…Such dynamics in abundance might be attributable to top-down control, namely grazing and viral lysis, yet unfortunately, no data is available for the viral and predators’ communities during the study period. Recent observations reported hypolimnion-specific heterotrophic nanoflagellate communities ( Mukherjee et al, 2015 , 2017 ) that might be grazing on CL500-11. Larger mixotrophic flagellates and ciliates may also be the major predator of CL500-11, as they can efficiently graze bacterioplankton of this size as well ( Posch et al, 1999 ).…”

Section: Resultsmentioning

confidence: 99%

The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes

et al. 2018

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CL500-11 (phylum Chloroflexi) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken vertically (5–12 depths in each lake) and temporally (in two lakes) at the deepest point of the lakes located in Switzerland, Italy, and Austria with varying depth, trophic state, mixing regime, and water retention time. The results showed a dominance of CL500-11 in all the lakes; their proportion to total prokaryotes ranged from 4.3% (Mondsee) to 24.3% (Lake Garda) and their abundance ranged from 0.65 × 105 (Mondsee) to 1.77 × 105 (Lake Garda) cells mL-1. By summarizing available information on CL500-11 occurrence to date, we demonstrated their broad habitat spectrum, ranging from ultra-oligotrophic to meso-eutrophic lakes, while low abundances or complete absence was observed in lakes with shallow depth, low pH, and/or short water retention time (<1 year). Together with available metagenomic and geochemical evidences from literatures, here we reviewed potential substrates supporting growth of CL500-11. Overall, the present study further endorsed ubiquity and quantitative significance of CL500-11 in deep freshwater systems and narrowed the focus on their physiological characteristics and ecological importance.

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Section: Resultsmentioning

confidence: 99%

The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes

et al. 2018

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“…This seasonal community variation in different depths presents an interesting ecosystem to understand the ecology of these microorganisms. However there are only a few studies on freshwater deep lakes, and the microbial communities in the hypolimnion waters are poorly understood (Okazaki and Nakano, 2016; Mukherjee et al, 2017). The limited number of studies that have been conducted on the oxygenated hypolimnion of freshwater deep lakes have studied bacterial community, where they reported the dominance of hypolimnion-specific bacterial lineages (Urbach et al, 2001; Callieri et al, 2015; Okazaki et al, 2017; Mehrshad et al, 2018; Andrei et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Information about the protist communities in hypolimnion waters is poorly known. However, the limited information available about the protist communities in the oxygenated hypolimnion waters of some deep holomictic lakes also indicates the dominance of hypolimnion-specific lineages (Lepère et al, 2010; Mukherjee et al, 2015, 2017).…”

Section: Introductionmentioning

confidence: 99%

Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes

et al. 2019

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Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters.

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“…Phytoplankton and the components of the microbial food web (bacteria and protozoa) were considered as potential food sources for rotifers [6]. At this time, since we could not find a suitable primer to detect only heterotrophic nanoflagellates (HNF) specifically, we applied a universal primer for eukaryotes to HNF [38,39]. PCR conditions for each primer in a thermal cycler (Bio-rad, California, USA) were summarized in Table 2.…”

Section: Dna Analysis Precedurementioning

confidence: 99%

Pretreatment Method for DNA Barcoding to Analyze Gut Contents of Rotifers

Krogh

Jeong

et al. 2020

Applied Sciences

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We designed an experiment to analyze the gut content of Rotifera based on DNA barcoding and tested it on Asplanchna sp. in order to ensure that the DNA extracted from the rotifer species is from the food sources within the gut. We selected ethanol fixation (60%) to minimize the inflow effects of treated chemicals, and commercial bleach (the final concentration of 2.5%, for 210 s) to eliminate the extracellular DNA without damage to the lorica. Rotifers have different lorica structures and thicknesses. Therefore, we chose a pretreatment method based on Asplanchna sp., which is known to have weak durability. When we used the determined method on a reservoir water sample, we confirmed that the DNA fragments of Chlorophyceae, Diatomea, Cyanobacteria, and Ciliophora were removed. Given this result, Diatomea and cyanobacteria, detected from Asplanchna, can be considered as gut contents. However, bacteria were not removed by bleach, thus there was still insufficient information. Since the results of applying commercial bleach to rotifer species confirmed that pretreatment worked effectively for some species of rotifers food sources, in further studies, it is believed to be applicable to the gut contents analysis of more diverse rotifers species and better DNA analysis techniques by supplementing more rigorous limitations.

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Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan

Cited by 16 publications

References 90 publications

The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes

The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes

Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes

Pretreatment Method for DNA Barcoding to Analyze Gut Contents of Rotifers

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